Genes and pathways differentially expressed in bipolar disorder and/or major depressive disorder

ABSTRACT

The present invention provides methods for diagnosing mental disorders. The invention also provides methods of identifying modulators of mental disorders as well as methods of using these modulators to treat patients suffering from mental disorders.

CROSS-REFERENCES TO RELATED APPLICATIONS

The present application is related to U.S. Ser. No. 60/581,998, filedJun. 21, 2004, and U.S. Ser. No. 60/621,252, filed Oct. 22, 2004, andU.S. Ser. No. 60/667,296, filed Mar. 31, 2005 each of which isincorporated herein in its entirety by reference.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

Not applicable.

BACKGROUND OF THE INVENTION

Clinical depression, including both bipolar disorders and majordepression disorders, is a major public health problem, affecting anestimated 9.5% of the adult population of the United States each year.While it has been hypothesized that mental illness, including mooddisorders such as major depression (“MDD”) and bipolar disorder (“BP”)as well as psychotic disorders such as schizophrenia, may have geneticroots, little progress has been made in identifying gene sequences andgene products that play a role in causing these disorders, as is truefor many diseases with a complex genetic origin (see, e.g., Burmeister,Biol. Psychiatry 45:522-532 (1999)).

The current lack of biomarkers and the ineffectiveness and reliabilityof the diagnosis and rates are important issues for the treatment ofmental disorders. For example, around 15% of the population suffers fromMDD while approximately 1% suffers from BP disorders. Diagnosing bipolardisorder is difficult when, as sometimes occurs, the patient presentsonly symptoms of depression to the clinician. At least 10-15% of BPpatients are reported to be misdiagnosed as MDD. The consequences ofsuch misdiagnosis include a delay in being introduced to efficacioustreatment with mood stabilizers and a delay in seeking or obtainingcounseling specific to bipolar disorder. Also treatment withantidepressants alone induces rapid cycling, switching to manic or mixedstate, and consequently increases suicide risk. Furthermore, in additionto a lack of efficacy, long onset of action and side effects (sexual,sleep, weight gain, etc.), there are recent concerns relating to theundesirable effects of ADs on metabolic syndromes, such as diabetes andhypercholesteremia.

BRIEF SUMMARY OF THE INVENTION

Relying on the discovery that certain genes expressed in particularbrain pathways and regions are likely involved in the development ofmental illness, the present invention provides methods for diagnosis andtreatment of mental illness, as well as methods for identifyingcompounds effective in treating mental illness.

In order to further understand the neurobiology of mood disorders suchas bipolar disorders (BP) and major depression disorders (MDD), theinventors of the present application have used DNA microarrays to studyexpression profiles of human post-mortem brains from patients diagnosedwith BP or MDD. In one aspect, the present invention relates todifferential gene expression in the Anterior Cingulate (AnCg),Dorsolateral Prefrontal (DLPFC), and Cerebellar (CB) cortices,Hippocampus, Nucleus Accumbens and Amygdala regions of the brain,wherein the differential gene expression is associated with BipolarDisorder (BPD) and Major Depressive Disorder (MDD). Certain genes inthese regions are considered “unique” to a given disorder such as BP orMDD when differentially expressed in a particular mood disorder and notanother (see, e.g., Tables 3, 4, 14-20). In other cases, where the genesare differentially expressed in both BP and MDD relative to healthycontrols, the genes are considered to be involved in both disorders.Expression of the differentially expressed genes may be detected usingany suitable methods of detection, e.g., microarrays, PCR or in situhybridization. Gene expression may be detected in brain tissue, braintissue samples, or other tissue samples (e.g., blood samples in the caseof NCAM1).

In one aspect, the present invention relates to differential geneexpression associated with G protein-coupled receptors (GPCR)s anddownstream signaling pathways, mediated by cyclic adenosinemonophosphate (cAMP) and phosphatidylinositol (PI), wherein the geneexpression differentially occurs in the Anterior Cingulate (AnCg),Dorsolateral Prefrontal (DLPFC), and Cerebellar (CB) cortices,Hippocampus, Nucleus Accumbens and Amygdala regions of the brains ofpatients with Bipolar Disorder (BPD) and/or Major Depressive Disorder(MDD), relative to healthy controls (see, e.g., Tables 14-20).

In another aspect, the present invention relates to differential geneexpression associated with G protein-coupled receptors (GPCR)s anddownstream signaling pathways, mediated by cyclic adenosinemonophosphate (cAMP) and phosphatidylinositol (PI), wherein the geneexpression differentially occurs in the Hippocampus, Nucleus Accumbensand Amygdala regions of the brains of patients with Bipolar Disorder(BPD) and/or Major Depressive Disorder (MDD), relative to healthycontrols (see, e.g., Tables 18-20).

The present invention also demonstrates differential expression of theFGF pathway in the frontal cortex of MDD subjects. ParticularFGF-related genes, such as FGF2, are dysregulated by antidepressanttherapy, environmental complexity, and the correlation to anxiety-likebehavior (see, e.g., Tables 1a, 1b, and 2, and FIGS. 1-7 and 22). TheFGF pathway is also related to neurogenesis, e.g., neural stem cellproliferation and differentiation, and the genes disclosed herein can beused for diagnosis and therapeutics related to neurogenesis.Furthermore, FIG. 23 shows the effects of postnatal FGF-2 adminstrationon neurogenesis, emotionality and gene expression in adult rats. The FGFinjected animals exhibit significantly increased cell survival andproliteration in the dentate gyrus of the hippocampus. As adults, theanimals show higher locomotor activity in a novel environment, an indexof lower anxiety, and have better learning and memory.

The present invention also demonstrates that the genes of theglutamate/GABA signaling pathways are involved in MDD and BP (see FIG.24 and Table 8).

The present invention also demonstrates that mitrochondrial genes areinvolved in MDD andBP (see Table 10).

The present invention also demonstrates that 40 genes encoding growthfactor family members and growth factor receptors are significantlydifferentially expressed in BP or MDD in the DLPFC or AnCg (see Tables5, 6 and 7).

The present invention demonstrates that genes involved in G proteincoupled receptors and their downstream signaling pathways, includingcyclic AMP, phosphatidylinositol, and mitogen-activated protein kinasesignaling pathways are dysregulated in BP and/or MDD (see Tables 6 and 9and FIGS. 8-13 and 17-19).

Finally the present invention provides for the first time a novelinsertion/deletion polymporphism in the phosphoserine phosphatase-likegene (PSPHL) and demonstrates that a novel deletion polymorphism ofPSPHL is related to susceptibility to bipolar disorder. Therefore,detection of this polymorphism is useful for diagnosis of BP, as well asfor drug discovery assays for BP therapeutics. In addition, the serineamino acid metabolic pathway, of which PSPHL is a member, is a targetfor drug discovery for BP therapeutics. The PSPHL gene was first clonedby Planitzer et al., Gene 210 297-306 (1998). The accession number for arepresentative nucleic acid sequence is AJ0016112 and the accessionnumber for a representative protein sequence is CAA04865.1. See FIGS.14-16.

The present invention demonstrates, for the first time, uniqueexpression of the 24 nucleic acids listed in Table 3 in the brains ofbipolar disorder subjects but not major depression subjects; the uniqueexpression of the 24 nucleic acids listed in Table 4 in the brains ofmajor depression subjects but not bipolar subjects, and the differentialand/or unique expression of the nucleic acids listed in Tables 5-10 inthe brains of patients suffering from bipolar disorder and majordepression disorder, in comparison with normal control subjects. Inaddition, the present invention identifies biochemical pathways involvedin uniquely or differentially in mood disorders, where the proteinsencoded by the nucleic acids listed in Table 3-10 are components of thebiochemical pathways (e.g., the growth factor, e.g., FGF, signaltransduction pathway, GPCR signal transduction pathways, mitochondrialpathways, and glutamate/GABA signaling pathways). Furthermore, theinvention demonstrates the unique expression of a PSPHL deletionpolymorphism and it's associate with BP.

Genes and pathways that are uniquely or differentially expressed in MDDor BP are useful in diagnosing mood disorders and in assaying fortherapeutics that can specifically treat MDD or BP, or can be used totreat both MDD and BP. Differential expression by brain region similarlyis a useful diagnostic and therapeutic tool, as certain mood disordersprimarily affect certain brain regions. Each brain region plays a uniqueand critical role in the overall phenotype of any particular mooddisorder. Furthermore, because of the relationship between BP andpsychotic disorders such as schizo affective disorders, the genedescribed herein unique to BP can also be uniquely expressed inschizophrenia, and so can be used for differential diagnosis with MDD.

This invention thus provides methods for determining whether a subjecthas or is predisposed for a mental disorder such as bipolar disorder ormajor depression disorder. The invention also provides methods ofproviding a prognosis and for monitoring disease progression andtreatment. Furthermore, the present invention provides nucleic acid andprotein targets for assays for drugs for the treatment of mentaldisorders such as bipolar disorder and major depression disorder.

In some embodiments, the methods comprise the steps of: (i) obtaining abiological sample from a subject; (ii) contacting the sample with areagent that selectively associates with a polynucleotide or polypeptideencoded by a nucleic acid that hybridizes under stringent conditions toa nucleotide sequence listed in Tables 3-10 and FIG. 14; and (iii)detecting the level of reagent that selectively associates with thesample, thereby determining whether the subject has or is predisposedfor a mental disorder.

In some embodiments, the reagent is an antibody. In some embodiments,the reagent is a nucleic acid. In some embodiments, the reagentassociates with a polynucleotide. In some embodiments, the reagentassociates with a polypeptide. In some embodiments, the polynucleotidecomprises a nucleotide sequence listed in Table 3-6. In some embodiment,the polypeptide comprises an amino acid sequence of a gene listed inTable 3-6. In some embodiments, the level of reagent that associateswith the sample is different (i.e., higher or lower) from a levelassociated with humans without a mental disorder. In some embodiments,the biological sample is obtained from amniotic fluid. In someembodiments, the mental disorder is a mood disorder. In someembodiments, the mood disorder is selected from the group consisting ofbipolar disorder and major depression disorder.

The invention also provides methods of identifying a compound fortreatment of a mental disorder. In some embodiments, the methodscomprises the steps of: (i) contacting the compound with a polypeptide,which is encoded by a polynucleotide that hybridizes under stringentconditions to a nucleic acid comprising a nucleotide sequence of Table2, 3, or 4; and (ii) determining the functional effect of the compoundupon the polypeptide, thereby identifying a compound for treatment of amental disorder.

In some embodiments, the contacting step is performed in vitro. In someembodiment, the polypeptide comprises an amino acid sequence of a genelisted in Table 3-6. In some embodiments, the polypeptide is expressedin a cell or biological sample, and the cell or biological sample iscontacted with the compound. In some embodiments, the mental disorder isa mood disorder or psychotic disorder. In some embodiments, the mooddisorder is selected from the group consisting of bipolar disorder andmajor depression. In some embodiments, the psychotic disorder isschizophrenia. In some embodiments, the methods further compriseadministering the compound to an animal and determining the effect onthe animal, e.g., an invertebrate, a vertebrate, or a mammal. In someembodiments, the determining step comprises testing the animal's mentalfunction.

In some embodiments, the methods comprise the steps of (i) contactingthe compound to a cell, the cell comprising a polynucleotide thathybridizes under stringent conditions to a nucleotide sequence of Table3-6; and (ii) selecting a compound that modulates expression of thepolynucleotide, thereby identifying a compound for treatment of a mentaldisorder. In some embodiments, the polynucleotide comprises a nucleotidesequence listed in Table 3-6. In some embodiment, the expression of thepolynucleotide is enhanced. In some embodiments, the expression of thepolynucleotide is decreased. In some embodiments, the methods furthercomprise administering the compound to an animal and determining theeffect on the animal. In some embodiments, the determining stepcomprises testing the animal's mental function. In some embodiments, themental disorder is a mood disorder or a psychotic disorder. In someembodiments, the mood disorder is selected from the group consisting ofbipolar disorder and major depression. In some embodiments, thepsychotic disorder is schizophrenia.

The invention also provides methods of treating a mental disorder in asubject. In some embodiments, the methods comprise the step ofadministering to the subject a therapeutically effective amount of acompound identified using the methods described above. In someembodiments, the mental disorder is a mood disorder or a psychoticdisorder. In some embodiments, the mood disorder is selected from thegroup consisting of bipolar disorder and major depression. In someembodiments, the psychotic disorder is schizophrenia. In someembodiments, the compound is a small organic molecule, an antibody, anantisense molecule, or a peptide.

The invention also provides methods of treating mental illness in asubject, comprising the step of administering to the subject atherapeutically effective amount of a polypeptide, which is encoded by apolypeptide that hybridizes under stringent conditions to a nucleic acidof Table 3-6. In some embodiments, the polypeptide comprises an aminoacid sequence encoded by a gene listed in Table 3-6. In someembodiments, the mental illness is a mood disorder or a psychoticdisorder. In some embodiments, the psychotic disorder is schizophrenia.In some embodiments, the mood disorder is a bipolar disorder or majordepression.

The invention also provides methods of treating mental illness in asubject, comprising the step of administering to the subject atherapeutically effective amount of a polypeptide, wherein thepolypeptide hybridizes under stringent conditions to a nucleic acid ofTable 3-6. In some embodiments, the mental illness is a mood disorder ora psychotic disorder. In some embodiments, the psychotic disorder isschizophrenia. In some embodiments, the mood disorder is a bipolardisorder or major depression.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Rodent FGFR2 ISH. Graph shows mean grayscale (n=6 per group)intensity and standard error bars for 35 S signal for regions indicatedfor both fluoxetine treated and saline treated rats. The increase insignal in the fluoxetine treated group is significant as determined boya tow-way ANOVA (treatment, brain region) with p=0.0049, Fisher's PLSD.

FIG. 2: FIG. 2 summarizes differential expression of FGF systemtranscripts in MDD cortex.

FIG. 3: FIG. 3 shows FGF dysregulation is attenuated by anti-depressanttherapy.

FIG. 4: FIG. 4 shows that chronic fluoxetine treatment increases FGFR2expression in rat forebrain.

FIG. 5: FIG. 5 shows environmental complexity: FGF2 and anxiety-likebehavior.

FIG. 6: FIG. 6 shows FGF expression negatively correlates withanxiety-like behavior.

FIG. 7: FIG. 7 shows summarizes FGF and negative affect.

FIG. 8: FIG. 8 shows qRT-PCR validation of microarray data.

FIG. 9: FIG. 9 shows G-protein coupled receptor (GPCR) and ligandsdysregulated in anterior cingulated cortex of BP subjects.

FIG. 10: shows gene category over-representation analysis of the threedownstream GPCR signaling pathways.

FIG. 11: FIG. 11 shows phosphatidylinositol metabolism in BP disorder.

FIG. 12: FIG. 12 shows mitogen activated protein kinase signaling in BPdisorder.

FIG. 13: FIG. 13 shows cAMP signaling pathway in BP subjects

FIG. 14: FIG. 14 shows genomic structure of the PSPHL gene and thedeletion polymorphism of PSPHL that is related to BP susceptibility.

FIG. 15: FIG. 15 shows the predicted amino acid sequences for PSPH,PSPHL-A, and PSPHL-B.

FIG. 16: FIG. 16 shows the serine amino acid metabolic pathway.

FIG. 17: FIG. 17 shows where each exon begins and ends in the PSPHL mRNAand provides primers to detect insertion/deletion polymorphisms in thePSPHL locus.

FIG. 18: FIG. 18 shows a gel image for PSPHL insertion/deletion alleles.

FIG. 19: FIG. 19 shows the cAMP signaling pathway in the limbic systemfor BP.

FIG. 20: FIG. 20 shows the PI signaling pathway in the limbic system forMDD.

FIG. 21: FIG. 21 shows MAPK signaling pathway in the limbic system forMDD.

FIG. 22: FIG. 22 shows the effects of environmental complexity ondifferences in anxiety behavior and FGF2 gene expression.

FIG. 23: FIG. 23 shows the effects of postnatal FGF2 administration onneurogenesis, emotionality and gene expression in adult rats.

FIG. 24: FIG. 24 shows GABA/glutamate signaling pathways in BP and MDD.

FIG. 25: FIG. 25 shows NCAM SNPs and splice variants involved in mooddisorders such as bipolar disorder.

FIG. 26: The figure summarizes differential expressed genes regulatingcAMP-(A, B) and phosphatidylinositol-(C, D) signaling pathways in thebrain of BPD (A, C) and MDD (B, D). GNAI1: G protein alpha inhibitingactivity 1, RGS20: Regulator of G-protein signaling 20, PDE1A:Phosphodiesterase 1A, PDE8A: Phosphodiesterase 8A, PKIA: Protein kinaseA inhibitor alpha, CDK5: Cyclin-dependent kinase 5, PPP1CA: Proteinphosphatase 1, catalytic alpha, PPPlR3C: Protein phosphatase 1,regulatory 3C, INPP5A: Inositol polyphosphate-5-phosphatase A, INPP5F:Inositol polyphosphate-5-phosphatase F, ITPKB: Inositol1,4,5-trisphosphate 3-kinase B, INPP1: Inositolpolyphosphate-1-phosphatase, CDS 1: CDP-diacylglycerol synthase 1,PIK3C2A: Phosphoinositide-3-kinase catalytic 2A, PIK3C2B:Phosphoinositide-3-kinase catalytic 2B, PIK3R1:Phosphoinositide-3-kinase regulatory 1, PRKCI: Protein kinase C iota,ITPR1: Inositol 1,4,5-triphosphate receptor 1, PRKB 1: Protein kinase Cbeta 1, NPY: Neuropeptide Y, SST: Somatostatin, NPY1R: Neuropeptide Yreceptor Y1, TACR2: Tachykinin receptor 2, NTSR2: Neurotensin receptor2, EDNRB: Endothelin receptor type B, GRM3: Metabotropic Glutamatereceptor 3, EDG1: Endothelial differentiation GPCR 1, EDG2: Endothelialdifferentiation GPCR 2.

FIG. 27: In situ hybridization images of GPR37 mRNA in representativeBPD, MDD and control subjects GPR37 mRNA is preferentially expressed insubcortical white matter. Among 6 layers of cortical gray matter, GPR37expression in deeper layer (V-VI) is relatively higher than superficiallayer (I-III). Expression levels in GPR37 is increased in the BPDsubjects, and decreased in MDD subjects in subcortical white matter inanterior cingulate cortex tissue, compared to control subjects. WM:Subcortical white matter, BPD: Bipolar disorder, MDD: Major depressivedisorder.

FIGS. 28 and 29: In situ hybridization for LRPPRC (leucine-richPPR-motif containing) mRNA in three brain regions. (A). LRPPRCexpression in BPD and control representative images. (B). Controls withagonal factors showed a 36% reduction in LRPPRC compared to controlswith zero agonal factors (p=0.011) in cerebellum and a similar effectwas seen across the cortical regions. (C). In DLPFC, the BPD caseswithout agonal factors show increased LRPPRC compared to controlswithout agonal factors (p=0.001) and compared to MDD subjects (p=0.02)without agonal factors.

FIG. 30: NCAM1 (i.e., neural cell adhesion molecule 1) genomicorganization and location of four polymorphic sites. The gene spans 214kb, but does not contain any exonic SNPs. The arrows indicate thelocation of the four polymorphisms and the five exons used in thisexploratory analysis.

FIG. 31: Significant alterations of NCAMI exon splice variant levels areshown by genotype and diagnosis by genotype.

TABLE LEGENDS

Table 1a: Table 1a lists subject data for cohort A.

Table 1b: Table 1b lists subject data for cohort B.

Table 2: Table 2 shows microarray data for all FGF transcripts detectedin either DLPFC or AnCg and summary data for confirmation studies.

Table 3: Table 3 lists genes uniquely expressed in BP subjects.

Table 4: Table 4 lists genes uniquely expressed in MDD subjects.

Table 5: Table 5 lists growth factor pathway genes expressed in MDD andBP subjects.

Table 6: Table 6 lists GPCR pathway genes expressed in MDD and BPsubjects.

Table 7: Table 7 lists growth factor pathway genes expressed in MDD andBP subjects.

Table 8: Table 8 lists GABA and glutamate signaling pathway genesexpressed in MDD and BP subjects.

Table 9: Table 9 lists GPCR pathway genes expressed in MDD and BPsubjects.

Table 10: Table 10 lists mitochondrial genes expressed in MDD and BPsubjects.

Table 11: Table 11 lists genes expressed in MDD, BP, and schizophreniasubjects.

Table 12: Table 12 lists genes expressed in MDD, BP, and schizophreniasubjects.

Table 13: Table 13 lists GPCR pathway genes expressed in MDD and BP.

Table 14: GPCRs and related signaling genes dysregulated in anteriorcingulate cortex.

Table 15: GPCRs and related signaling genes dysregulated in dorsolateralprefrontal cortex.

Table 16: GPCRs and related signaling genes dysregulated in cerebellarcortex.

Table 17: Quantitative RT-PCR data. Fold changes in microarray andqRT-PCR analyses for representative ligand peptides, GPCRs, G proteinregulator (NPY, SST, GPR37, GPRC5B, RGS20), which were dysregulated inBPD/MDD compared to the control group. N.S., No significant change; *.p<0.05; **, p<0.01.

Table 18: GPCRs and related signaling genes dysregulated in amygdala,hippocampus, nucleus accumbens of BPD.

Table 19: GPCRs and related signaling genes dysregulated in amygdala,hippocampus, nucleus accumbens of MDD.

Table 20: Table 20 shows the genes that were differentially expressed inBPD or MDD by >1.2 fold change and were down-regulated in agonal factorcontrol comparisons by <1.0. The opposite genes are also shown, wherethere was a decrease in mood disorder by ←1.2 fold change, and theagonal factor control comparison showed an increase >1.0 fold change.These genes were found in 4 major classifications listed: mitochondria,chaperone, apoptosis, and proteasome.

Table 21: Real time Q-PCR validation results for selected mitochondrialrelated candidate genes for mood disorders in two cortical regions.These genes are nuclear-encoded. Significant by Q-PCR p<0.05 one-tailedt-test. The Q-PCR t-test MDD, BPD, and control groups used subjects withno agonal factors and pH>6.8 similar to microarray analysis #3 groupsMDD-High, BPD-High, and Control-High.

Table 22: Mitochondrial DNA (mtDNA) encoded genes were analyzed by realtime Q-PCR for differential expression in BPD and MDD compared tocontrols. Nuclear encoded genes in BPD and MDD subjects appeared togenerally be increased while several mtDNA genes showed a significantdecrease by Q-PCR in mood disorders.

Table 23: Primers for each DNA segment and possible combination ofsplice variants (a, b, c, SEC and VASE), as well as, for SNP 9 and anexon outside of the splice sites for measuring total NCAM1. Thenumbering is shown in FIG. 26 according to accession M22094. * 1—Onlythe forward primer could be designed because exon a is 14 bps. 2—Exon 3is before the variable exons and only the forward primer was needed toPCR outside the exons. 3—Exon 8 is after the variable exons and only thereverse primer was needed to PCR outside the exons.

Table 24: Genotypic Association Results. The odds ratio, chi-square(chi2) and p-values where all calculated using the DeFinetti programTests for Deviation from HWE and Tests for Association (C.I.: 95%confidence interval).

Table 25: SNP 9 and SNP b haplotype frequency, odds ratio and p-values.P-values were calculated from the Chi-squared values derived from theEHplus program.

Table 26: Genotypic and Allelic Distributions for Controls, BipolarDisorder and Schizophrenia. Fisher's exact p-values are shown forallelic distribution between case-controls.

Table 27: Genotype×Splice Variant Differences×Diagnosis (p-values). Foreach SNP genotype and splice variant the splice variant amounts wereevaluated by t-test based on diagnosis and the significant p-values werereported.

Tables 28: Genes upregulated (28.1) and downregulated (28.2) by Lithiumin monkey brains.

Table 29: Values of V-ATPase Subunits differential expression inNon-human primate model of depression.

Table 30: Genes differentially expressed in the frontal cortex of ratssubjected to chronic unpredictable stress (CUS) and antidepressantadministration (All=fluoxetine, desipramine, and bupropion). Controlswere administered water (H2O treated).

DEFINITIONS

A “mental disorder” or “mental illness” or “mental disease” or“psychiatric or neuropsychiatric disease or illness or disorder” refersto mood disorders (e.g., major depression, mania, and bipolardisorders), psychotic disorders (e.g., schizophrenia, schizoaffectivedisorder, schizophreniform disorder, delusional disorder, briefpsychotic disorder, and shared psychotic disorder), personalitydisorders, anxiety disorders (e.g., obsessive-compulsive disorder) aswell as other mental disorders such as substance-related disorders,childhood disorders, dementia, autistic disorder, adjustment disorder,delirium, multi-infarct dementia, and Tourette's disorder as describedin Diagnostic and Statistical Manual of Mental Disorders, FourthEdition, (DSM IV). Typically, such disorders have a complex geneticand/or a biochemical component.

A “mood disorder” refers to disruption of feeling tone or emotionalstate experienced by an individual for an extensive period of time. Mooddisorders include major depression disorder (i.e., unipolar disorder),mania, dysphoria, bipolar disorder, dysthymia, cyclothymia and manyothers. See, e.g., Diagnostic and Statistical Manual of MentalDisorders, Fourth Edition, (DSM IV).

“Major depression disorder,” “major depressive disorder,” or “unipolardisorder” refers to a mood disorder involving any of the followingsymptoms: persistent sad, anxious, or “empty” mood; feelings ofhopelessness or pessimism; feelings of guilt, worthlessness, orhelplessness; loss of interest or pleasure in hobbies and activitiesthat were once enjoyed, including sex; decreased energy, fatigue, being“slowed down”; difficulty concentrating, remembering, or makingdecisions; insomnia, early-morning awakening, or oversleeping; appetiteand/or weight loss or overeating and weight gain; thoughts of death orsuicide or suicide attempts; restlessness or irritability; or persistentphysical symptoms that do not respond to treatment, such as headaches,digestive disorders, and chronic pain. Various subtypes of depressionare described in, e.g., DSM IV.

“Bipolar disorder” is a mood disorder characterized by alternatingperiods of extreme moods. A person with bipolar disorder experiencescycling of moods that usually swing from being overly elated orirritable (mania) to sad and hopeless (depression) and then back again,with periods of normal mood in between. Diagnosis of bipolar disorder isdescribed in, e.g., DSM IV. Bipolar disorders include bipolar disorder I(mania with or without major depression) and bipolar disorder II(hypomania with major depression), see, e.g., DSM IV.

“A psychotic disorder” refers to a condition that affects the mind,resulting in at least some loss of contact with reality. Symptoms of apsychotic disorder include, e.g., hallucinations, changed behavior thatis not based on reality, delusions and the like. See, e.g., DSM IV.Schizophrenia, schizoaffective disorder, schizophreniform disorder,delusional disorder, brief psychotic disorder, substance-inducedpsychotic disorder, and shared psychotic disorder are examples ofpsychotic disorders.

“Schizophrenia” refers to a psychotic disorder involving a withdrawalfrom reality by an individual. Symptoms comprise for at least a part ofa month two or more of the following symptoms: delusions (only onesymptom is required if a delusion is bizarre, such as being abducted ina space ship from the sun); hallucinations (only one symptom is requiredif hallucinations are of at least two voices talking to one another orof a voice that keeps up a running commentary on the patient's thoughtsor actions); disorganized speech (e.g., frequent derailment orincoherence); grossly disorganized or catatonic behavior; or negativesymptoms, i.e., affective flattening, alogia, or avolition.Schizophrenia encompasses disorders such as, e.g., schizoaffectivedisorders. Diagnosis of schizophrenia is described in, e.g., DSM IV.Types of schizophrenia include, e.g., paranoid, disorganized, catatonic,undifferentiated, and residual.

An “antidepressant” refers to an agents typically used to treat clinicaldepression. Antidepressants includes compounds of different classesincluding, for example, specific serotonin reuptake inhibitors (e.g.,fluoxetine), tricyclic antidepressants (e.g., desipramine), and dopaminereuptake inhibitors (e.g, bupropion). Typically, antidepressants ofdifferent classes exert their therapeutic effects via differentbiochemical pathways. Often these biochemical pathways overlap orintersect. Additonal diseases or disorders often treated withantidepressants include, chronic pain, anxiety disorders, and hotflashes.

An “agonist” refers to an agent that binds to a polypeptide orpolynucleotide of the invention, stimulates, increases, activates,facilitates, enhances activation, sensitizes or up regulates theactivity or expression of a polypeptide or polynucleotide of theinvention.

An “antagonist” refers to an agent that inhibits expression of apolypeptide or polynucleotide of the invention or binds to, partially ortotally blocks stimulation, decreases, prevents, delays activation,inactivates, desensitizes, or down regulates the activity of apolypeptide or polynucleotide of the invention.

“Inhibitors,” “activators,” and “modulators” of expression or ofactivity are used to refer to inhibitory, activating, or modulatingmolecules, respectively, identified using in vitro and in vivo assaysfor expression or activity, e.g., ligands, agonists, antagonists, andtheir homologs and mimetics. The term “modulator” includes inhibitorsand activators. Inhibitors are agents that, e.g., inhibit expression ofa polypeptide or polynucleotide of the invention or bind to, partiallyor totally block stimulation or enzymatic activity, decrease, prevent,delay activation, inactivate, desensitize, or down regulate the activityof a polypeptide or polynucleotide of the invention, e.g., antagonists.Activators are agents that, e.g., induce or activate the expression of apolypeptide or polynucleotide of the invention or bind to, stimulate,increase, open, activate, facilitate, enhance activation or enzymaticactivity, sensitize or up regulate the activity of a polypeptide orpolynucleotide of the invention, e.g., agonists. Modulators includenaturally occurring and synthetic ligands, antagonists, agonists, smallchemical molecules and the like. Assays to identify inhibitors andactivators include, e.g., applying putative modulator compounds tocells, in the presence or absence of a polypeptide or polynucleotide ofthe invention and then determining the functional effects on apolypeptide or polynucleotide of the invention activity. Samples orassays comprising a polypeptide or polynucleotide of the invention thatare treated with a potential activator, inhibitor, or modulator arecompared to control samples without the inhibitor, activator, ormodulator to examine the extent of effect. Control samples (untreatedwith modulators) are assigned a relative activity value of 100%.Inhibition is achieved when the activity value of a polypeptide orpolynucleotide of the invention relative to the control is about 80%,optionally 50% or 25-1%. Activation is achieved when the activity valueof a polypeptide or polynucleotide of the invention relative to thecontrol is 110%, optionally 150%, optionally 200-500%, or 1000-3000%higher.

The term “test compound” or “drug candidate” or “modulator” orgrammatical equivalents as used herein describes any molecule, eithernaturally occurring or synthetic, e.g., protein, oligopeptide (e.g.,from about 5 to about 25 amino acids in length, preferably from about 10to 20 or 12 to 18 amino acids in length, preferably 12, 15, or 18 aminoacids in length), small organic molecule, polysaccharide, lipid, fattyacid, polynucleotide, RNAi, oligonucleotide, etc. The test compound canbe in the form of a library of test compounds, such as a combinatorialor randomized library that provides a sufficient range of diversity.Test compounds are optionally linked to a fusion partner, e.g.,targeting compounds, rescue compounds, dimerization compounds,stabilizing compounds, addressable compounds, and other functionalmoieties. Conventionally, new chemical entities with useful propertiesare generated by identifying a test compound (called a “lead compound”)with some desirable property or activity, e.g., inhibiting activity,creating variants of the lead compound, and evaluating the property andactivity of those variant compounds. Often, high throughput screening(HTS) methods are employed for such an analysis.

A “small organic molecule” refers to an organic molecule, eithernaturally occurring or synthetic, that has a molecular weight of morethan about 50 Daltons and less than about 2500 Daltons, preferably lessthan about 2000 Daltons, preferably between about 100 to about 1000Daltons, more preferably between about 200 to about 500 Daltons.

An “siRNA” or “RNAi” refers to a nucleic acid that forms a doublestranded RNA, which double stranded RNA has the ability to reduce orinhibit expression of a gene or target gene when the siRNA expressed inthe same cell as the gene or target gene. “siRNA” or “RNAi” thus refersto the double stranded RNA formed by the complementary strands. Thecomplementary portions of the siRNA that hybridize to form the doublestranded molecule typically have substantial or complete identity. Inone embodiment, an siRNA refers to a nucleic acid that has substantialor complete identity to a target gene and forms a double stranded siRNA.Typically, the siRNA is at least about 15-50 nucleotides in length(e.g., each complementary sequence of the double stranded siRNA is 15-50nucleotides in length, and the double stranded siRNA is about 15-50 basepairs in length, preferable about preferably about 20-30 basenucleotides, preferably about 20-25 or about 24-29 nucleotides inlength, e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotidesin length.

“Determining the functional effect” refers to assaying for a compoundthat increases or decreases a parameter that is indirectly or directlyunder the influence of a polynucleotide or polypeptide of the invention(such as a polynucleotide of Table 3-6 or a polypeptide encoded by agene of Table 3-6), e.g., measuring physical and chemical or phenotypiceffects. Such functional effects can be measured by any means known tothose skilled in the art, e.g., changes in spectroscopic (e.g.,fluorescence, absorbance, refractive index), hydrodynamic (e.g., shape),chromatographic, or solubility properties for the protein; measuringinducible markers or transcriptional activation of the protein;measuring binding activity or binding assays, e.g. binding toantibodies; measuring changes in ligand binding affinity; measurement ofcalcium influx; measurement of the accumulation of an enzymatic productof a polypeptide of the invention or depletion of an substrate;measurement of changes in protein levels of a polypeptide of theinvention; measurement of RNA stability; G-protein binding; GPCRphosphorylation or dephosphorylation; signal transduction, e.g.,receptor-ligand interactions, second messenger concentrations (e.g.,cAMP, IP3, or intracellular Ca²⁺); identification of downstream orreporter gene expression (CAT, luciferase, β-gal, GFP and the like),e.g., via chemiluminescence, fluorescence, colorimetric reactions,antibody binding, inducible markers, and ligand binding assays.

Samples or assays comprising a nucleic acid or protein disclosed hereinthat are treated with a potential activator, inhibitor, or modulator arecompared to control samples without the inhibitor, activator, ormodulator to examine the extent of inhibition. Control samples(untreated with inhibitors) are assigned a relative protein activityvalue of 100%. Inhibition is achieved when the activity value relativeto the control is about 80%, preferably 50%, more preferably 25-0%.Activation is achieved when the activity value relative to the control(untreated with activators) is 110%, more preferably 150%, morepreferably 200-500% (i.e., two to five fold higher relative to thecontrol), more preferably 1000-3000% higher.

“Biological sample” includes sections of tissues such as biopsy andautopsy samples, and frozen sections taken for histologic purposes. Suchsamples include blood, sputum, tissue, lysed cells, brain biopsy,cultured cells, e.g., primary cultures, explants, and transformed cells,stool, urine, etc. A biological sample is typically obtained from aeukaryotic organism, most preferably a mammal such as a primate, e.g.,chimpanzee or human; cow; dog; cat; a rodent, e.g., guinea pig, rat,mouse; rabbit; or a bird; reptile; or fish.

“Antibody” refers to a polypeptide substantially encoded by animmunoglobulin gene or immunoglobulin genes, or fragments thereof whichspecifically bind and recognize an analyte (antigen). The recognizedimmunoglobulin genes include the kappa, lambda, alpha, gamma, delta,epsilon and mu constant region genes, as well as the myriadimmunoglobulin variable region genes. Light chains are classified aseither kappa or lambda. Heavy chains are classified as gamma, mu, alpha,delta, or epsilon, which in turn define the immunoglobulin classes, IgG,IgM, IgA, IgD and IgE, respectively.

An exemplary immunoglobulin (antibody) structural unit comprises atetramer. Each tetramer is composed of two identical pairs ofpolypeptide chains, each pair having one “light” (about 25 kD) and one“heavy” chain (about 50-70 kD). The N-terminus of each chain defines avariable region of about 100 to 110 or more amino acids primarilyresponsible for antigen recognition. The terms variable light chain(V_(L)) and variable heavy chain (V_(H)) refer to these light and heavychains respectively.

Antibodies exist, e.g., as intact immunoglobulins or as a number ofwell-characterized fragments produced by digestion with variouspeptidases. Thus, for example, pepsin digests an antibody below thedisulfide linkages in the hinge region to produce F(ab)′₂, a dimer ofFab which itself is a light chain joined to V_(H)-C_(H)1 by a disulfidebond. The F(ab)′₂ may be reduced under mild conditions to break thedisulfide linkage in the hinge region, thereby converting the F(ab)′₂dimer into an Fab′ monomer. The Fab′ monomer is essentially an Fab withpart of the hinge region (see, Paul (Ed.) Fundamental Immunology, ThirdEdition, Raven Press, NY (1993)). While various antibody fragments aredefined in terms of the digestion of an intact antibody, one of skillwill appreciate that such fragments may be synthesized de novo eitherchemically or by utilizing recombinant DNA methodology. Thus, the termantibody, as used herein, also includes antibody fragments eitherproduced by the modification of whole antibodies or those synthesized denovo using recombinant DNA methodologies (e.g., single chain Fv).

The terms “peptidomimetic” and “mimetic” refer to a synthetic chemicalcompound that has substantially the same structural and functionalcharacteristics of the polynucleotides, polypeptides, antagonists oragonists of the invention. Peptide analogs are commonly used in thepharmaceutical industry as non-peptide drugs with properties analogousto those of the template peptide. These types of non-peptide compoundare termed “peptide mimetics” or “peptidomimetics” (Fauchere, Adv. DrugRes. 15:29 (1986); Veber and Freidinger TINS p. 392 (1985); and Evans etal., J. Med. Chem. 30:1229 (1987), which are incorporated herein byreference). Peptide mimetics that are structurally similar totherapeutically useful peptides may be used to produce an equivalent orenhanced therapeutic or prophylactic effect. Generally, peptidomimeticsare structurally similar to a paradigm polypeptide (i.e., a polypeptidethat has a biological or pharmacological activity), such as a CCX CKR,but have one or more peptide linkages optionally replaced by a linkageselected from the group consisting of, e.g., —CH₂NH—, —CH₂S—, —CH₂—CH₂—,—CH═CH— (cis and trans), —COCH₂—, —CH(OH)CH₂—, and —CH₂SO—. The mimeticcan be either entirely composed of synthetic, non-natural analogues ofamino acids, or, is a chimeric molecule of partly natural peptide aminoacids and partly non-natural analogs of amino acids. The mimetic canalso incorporate any amount of natural amino acid conservativesubstitutions as long as such substitutions also do not substantiallyalter the mimetic's structure and/or activity. For example, a mimeticcomposition is within the scope of the invention if it is capable ofcarrying out the binding or enzymatic activities of a polypeptide orpolynucleotide of the invention or inhibiting or increasing theenzymatic activity or expression of a polypeptide or polynucleotide ofthe invention.

The term “gene” means the segment of DNA involved in producing apolypeptide chain; it includes regions preceding and following thecoding region (leader and trailer) as well as intervening sequences(introns) between individual coding segments (exons).

The term “isolated,” when applied to a nucleic acid or protein, denotesthat the nucleic acid or protein is essentially free of other cellularcomponents with which it is associated in the natural state. It ispreferably in a homogeneous state although it can be in either a dry oraqueous solution. Purity and homogeneity are typically determined usinganalytical chemistry techniques such as polyacrylamide gelelectrophoresis or high performance liquid chromatography. A proteinthat is the predominant species present in a preparation issubstantially purified. In particular, an isolated gene is separatedfrom open reading frames that flank the gene and encode a protein otherthan the gene of interest. The term “purified” denotes that a nucleicacid or protein gives rise to essentially one band in an electrophoreticgel. Particularly, it means that the nucleic acid or protein is at least85% pure, more preferably at least 95% pure, and most preferably atleast 99% pure.

The term “nucleic acid” or “polynucleotide” refers todeoxyribonucleotides or ribonucleotides and polymers thereof in eithersingle- or double-stranded form. Unless specifically limited, the termencompasses nucleic acids containing known analogues of naturalnucleotides that have similar binding properties as the referencenucleic acid and are metabolized in a manner similar to naturallyoccurring nucleotides. Unless otherwise indicated, a particular nucleicacid sequence also implicitly encompasses conservatively modifiedvariants thereof (e.g., degenerate codon substitutions), alleles,orthologs, SNPs, and complementary sequences as well as the sequenceexplicitly indicated. Specifically, degenerate codon substitutions maybe achieved by generating sequences in which the third position of oneor more selected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991);Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Cassol et al.(1992); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The termnucleic acid is used interchangeably with gene, cDNA, and mRNA encodedby a gene.

The terms “polypeptide,” “peptide,” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidue is an artificial chemical mimetic of a corresponding naturallyoccurring amino acid, as well as to naturally occurring amino acidpolymers and non-naturally occurring amino acid polymers. As usedherein, the terms encompass amino acid chains of any length, includingfull-length proteins (i.e., antigens), wherein the amino acid residuesare linked by covalent peptide bonds.

The term “amino acid” refers to naturally occurring and synthetic aminoacids, as well as amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids.Naturally occurring amino acids are those encoded by the genetic code,as well as those amino acids that are later modified, e.g.,hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acidanalogs refers to compounds that have the same basic chemical structureas a naturally occurring amino acid, i.e., an α carbon that is bound toa hydrogen, a carboxyl group, an amino group, and an R group, e.g.,homoserine, norleucine, methionine sulfoxide, methionine methylsulfonium. Such analogs have modified R groups (e.g., norleucine) ormodified peptide backbones, but retain the same basic chemical structureas a naturally occurring amino acid. “Amino acid mimetics” refers tochemical compounds that have a structure that is different from thegeneral chemical structure of an amino acid, but that functions in amanner similar to a naturally occurring amino acid.

Amino acids may be referred to herein by either the commonly known threeletter symbols or by the one-letter symbols recommended by the IUPAC-IUBBiochemical Nomenclature Commission. Nucleotides, likewise, may bereferred to by their commonly accepted single-letter codes.

“Conservatively modified variants” applies to both amino acid andnucleic acid sequences. With respect to particular nucleic acidsequences, “conservatively modified variants” refers to those nucleicacids that encode identical or essentially identical amino acidsequences, or where the nucleic acid does not encode an amino acidsequence, to essentially identical sequences. Because of the degeneracyof the genetic code, a large number of functionally identical nucleicacids encode any given protein. For instance, the codons GCA, GCC, GCGand GCU all encode the amino acid alanine. Thus, at every position wherean alanine is specified by a codon, the codon can be altered to any ofthe corresponding codons described without altering the encodedpolypeptide. Such nucleic acid variations are “silent variations,” whichare one species of conservatively modified variations. Every nucleicacid sequence herein that encodes a polypeptide also describes everypossible silent variation of the nucleic acid. One of skill willrecognize that each codon in a nucleic acid (except AUG, which isordinarily the only codon for methionine, and TGG, which is ordinarilythe only codon for tryptophan) can be modified to yield a functionallyidentical molecule. Accordingly, each silent variation of a nucleic acidthat encodes a polypeptide is implicit in each described sequence.

As to amino acid sequences, one of skill will recognize that individualsubstitutions, deletions or additions to a nucleic acid, peptide,polypeptide, or protein sequence which alters, adds or deletes a singleamino acid or a small percentage of amino acids in the encoded sequenceis a “conservatively modified variant” where the alteration results inthe substitution of an amino acid with a chemically similar amino acid.Conservative substitution tables providing functionally similar aminoacids are well known in the art. Such conservatively modified variantsare in addition to and do not exclude polymorphic variants, interspecieshomologs, and alleles of the invention.

The following eight groups each contain amino acids that areconservative substitutions for one another:

-   1) Alanine (A), Glycine (G);-   2) Aspartic acid (D), Glutamic acid (E);-   3) Asparagine (N), Glutamine (Q);-   4) Arginine (R), Lysine (K);-   5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);-   6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);-   7) Serine (S), Threonine (T); and-   8) Cysteine (C), Methionine (M)-   (see, e.g., Creighton, Proteins (1984)).

“Percentage of sequence identity” is determined by comparing twooptimally aligned sequences over a comparison window, wherein theportion of the polynucleotide sequence in the comparison window maycomprise additions or deletions (i.e., gaps) as compared to thereference sequence (which does not comprise additions or deletions) foroptimal alignment of the two sequences. The percentage is calculated bydetermining the number of positions at which the identical nucleic acidbase or amino acid residue occurs in both sequences to yield the numberof matched positions, dividing the number of matched positions by thetotal number of positions in the window of comparison and multiplyingthe result by 100 to yield the percentage of sequence identity.

The terms “identical” or percent “identity,” in the context of two ormore nucleic acids or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same(i.e., 60% identity, optionally 65%, 70%, 75%, 80%, 85%, 90%, or 95%identity over a specified region), when compared and aligned for maximumcorrespondence over a comparison window, or designated region asmeasured using one of the following sequence comparison algorithms or bymanual alignment and visual inspection. Such sequences are then said tobe “substantially identical.” This definition also refers to thecomplement of a test sequence. Optionally, the identity exists over aregion that is at least about 50 nucleotides in length, or morepreferably over a region that is 100 to 500 or 1000 or more nucleotidesin length.

For sequence comparison, typically one sequence acts as a referencesequence, to which test sequences are compared. When using a sequencecomparison algorithm, test and reference sequences are entered into acomputer, subsequence coordinates are designated, if necessary, andsequence algorithm program parameters are designated. Default programparameters can be used, or alternative parameters can be designated. Thesequence comparison algorithm then calculates the percent sequenceidentities for the test sequences relative to the reference sequence,based on the program parameters.

A “comparison window”, as used herein, includes reference to a segmentof any one of the number of contiguous positions selected from the groupconsisting of from 20 to 600, usually about 50 to about 200, moreusually about 100 to about 150 in which a sequence may be compared to areference sequence of the same number of contiguous positions after thetwo sequences are optimally aligned. Methods of alignment of sequencesfor comparison are well known in the art. Optimal alignment of sequencesfor comparison can be conducted, e.g., by the local homology algorithmof Smith and Waterman (1970) Adv. Appl. Math. 2:482c, by the homologyalignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443,by the search for similarity method of Pearson and Lipman (1988) Proc.Nat'l. Acad. Sci. USA 85:2444, by computerized implementations of thesealgorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin GeneticsSoftware Package, Genetics Computer Group, 575 Science Dr., Madison,Wis.), or by manual alignment and visual inspection (see, e.g., Ausubelet al., Current Protocols in Molecular Biology (1995 supplement)).

An example of an algorithm that is suitable for determining percentsequence identity and sequence similarity are the BLAST and BLAST 2.0algorithms, which are described in Altschul et al. (1977) Nuc. AcidsRes. 25:3389-3402, and Altschul et al. (1990) J. Mol. Biol. 215:403-410,respectively. Software for performing BLAST analyses is publiclyavailable through the National Center for Biotechnology Information.This algorithm involves first identifying high scoring sequence pairs(HSPs) by identifying short words of length W in the query sequence,which either match or satisfy some positive-valued threshold score Twhen aligned with a word of the same length in a database sequence. T isreferred to as the neighborhood word score threshold (Altschul et al.,supra). These initial neighborhood word hits act as seeds for initiatingsearches to find longer HSPs containing them. The word hits are extendedin both directions along each sequence for as far as the cumulativealignment score can be increased. Cumulative scores are calculatedusing, for nucleotide sequences, the parameters M (reward score for apair of matching residues; always >0) and N (penalty score formismatching residues; always <0). For amino acid sequences, a scoringmatrix is used to calculate the cumulative score. Extension of the wordhits in each direction are halted when: the cumulative alignment scorefalls off by the quantity X from its maximum achieved value; thecumulative score goes to zero or below, due to the accumulation of oneor more negative-scoring residue alignments; or the end of eithersequence is reached. The BLAST algorithm parameters W, T, and Xdetermine the sensitivity and speed of the alignment. The BLASTN program(for nucleotide sequences) uses as defaults a wordlength (W) of 11, anexpectation (E) or 10, M=5, N=−4 and a comparison of both strands. Foramino acid sequences, the BLASTP program uses as defaults a wordlengthof 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (seeHenikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915)alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparisonof both strands.

The BLAST algorithm also performs a statistical analysis of thesimilarity between two sequences (see, e.g., Karlin and Altschul (1993)Proc. Natl. Acad. Sci. USA 90:5873-5787). One measure of similarityprovided by the BLAST algorithm is the smallest sum probability (P(N)),which provides an indication of the probability by which a match betweentwo nucleotide or amino acid sequences would occur by chance. Forexample, a nucleic acid is considered similar to a reference sequence ifthe smallest sum probability in a comparison of the test nucleic acid tothe reference nucleic acid is less than about 0.2, more preferably lessthan about 0.01, and most preferably less than about 0.001.

An indication that two nucleic acid sequences or polypeptides aresubstantially identical is that the polypeptide encoded by the firstnucleic acid is immunologically cross reactive with the antibodiesraised against the polypeptide encoded by the second nucleic acid, asdescribed below. Thus, a polypeptide is typically substantiallyidentical to a second polypeptide, for example, where the two peptidesdiffer only by conservative substitutions. Another indication that twonucleic acid sequences are substantially identical is that the twomolecules or their complements hybridize to each other under stringentconditions, as described below. Yet another indication that two nucleicacid sequences are substantially identical is that the same primers canbe used to amplify the sequence.

The phrase “selectively (or specifically) hybridizes to” refers to thebinding, duplexing, or hybridizing of a molecule only to a particularnucleotide sequence under stringent hybridization conditions when thatsequence is present in a complex mixture (e.g., total cellular orlibrary DNA or RNA).

The phrase “stringent hybridization conditions” refers to conditionsunder which a probe will hybridize to its target subsequence, typicallyin a complex mixture of nucleic acid, but to no other sequences.Stringent conditions are sequence-dependent and will be different indifferent circumstances. Longer sequences hybridize specifically athigher temperatures. An extensive guide to the hybridization of nucleicacids is found in Tijssen, Techniques in Biochemistry and MolecularBiology—Hybridization with Nucleic Probes, “Overview of principles ofhybridization and the strategy of nucleic acid assays” (1993).Generally, stringent conditions are selected to be about 5-10° C. lowerthan the thermal melting point (T_(m)) for the specific sequence at adefined ionic strength pH. The T_(m) is the temperature (under definedionic strength, pH, and nucleic concentration) at which 50% of theprobes complementary to the target hybridize to the target sequence atequilibrium (as the target sequences are present in excess, at T_(m),50% of the probes are occupied at equilibrium). Stringent conditionswill be those in which the salt concentration is less than about 1.0 Msodium ion, typically about 0.01 to 1.0 M sodium ion concentration (orother salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60°C. for long probes (e.g., greater than 50 nucleotides). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide. For selective or specific hybridization, apositive signal is at least two times background, optionally 10 timesbackground hybridization. Exemplary stringent hybridization conditionscan be as following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42°C., or 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and0.1% SDS at 65° C. Such washes can be performed for 5, 15, 30, 60, 120,or more minutes. Nucleic acids that hybridize to the genes listed inTables 3-10 and FIG. 14 are encompassed by the invention.

Nucleic acids that do not hybridize to each other under stringentconditions are still substantially identical if the polypeptides thatthey encode are substantially identical. This occurs, for example, whena copy of a nucleic acid is created using the maximum codon degeneracypermitted by the genetic code. In such cases, the nucleic acidstypically hybridize under moderately stringent hybridization conditions.Exemplary “moderately stringent hybridization conditions” include ahybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C.,and a wash in 1×SSC at 45° C. Such washes can be performed for 5, 15,30, 60, 120, or more minutes. A positive hybridization is at least twicebackground. Those of ordinary skill will readily recognize thatalternative hybridization and wash conditions can be utilized to provideconditions of similar stringency.

For PCR, a temperature of about 36° C. is typical for low stringencyamplification, although annealing temperatures may vary between about32° C. and 48° C. depending on primer length. For high stringency PCRamplification, a temperature of about 62° C. is typical, although highstringency annealing temperatures can range from about 50° C. to about65° C., depending on the primer length and specificity. Typical cycleconditions for both high and low stringency amplifications include adenaturation phase of 90° C.-95° C. for 30 sec-2 min., an annealingphase lasting 30 sec.-2 min., and an extension phase of about 72° C. for1-2 min. Protocols and guidelines for low and high stringencyamplification reactions are provided, e.g., in Innis et al., PCRProtocols, A Guide to Methods and Applications (1990).

The phrase “a nucleic acid sequence encoding” refers to a nucleic acidthat contains sequence information for a structural RNA such as rRNA, atRNA, or the primary amino acid sequence of a specific protein orpeptide, or a binding site for a trans-acting regulatory agent. Thisphrase specifically encompasses degenerate codons (i.e., differentcodons which encode a single amino acid) of the native sequence orsequences which may be introduced to conform with codon preference in aspecific host cell.

The term “recombinant” when used with reference, e.g., to a cell, ornucleic acid, protein, or vector, indicates that the cell, nucleic acid,protein or vector, has been modified by the introduction of aheterologous nucleic acid or protein or the alteration of a nativenucleic acid or protein, or that the cell is derived from a cell somodified. Thus, for example, recombinant cells express genes that arenot found within the native (nonrecombinant) form of the cell or expressnative genes that are otherwise abnormally expressed, under-expressed ornot expressed at all.

The term “heterologous” when used with reference to portions of anucleic acid indicates that the nucleic acid comprises two or moresubsequences that are not found in the same relationship to each otherin nature. For instance, the nucleic acid is typically recombinantlyproduced, having two or more sequences from unrelated genes arranged tomake a new functional nucleic acid, e.g., a promoter from one source anda coding region from another source. Similarly, a heterologous proteinindicates that the protein comprises two or more subsequences that arenot found in the same relationship to each other in nature (e.g., afusion protein).

An “expression vector” is a nucleic acid construct, generatedrecombinantly or synthetically, with a series of specified nucleic acidelements that permit transcription of a particular nucleic acid in ahost cell. The expression vector can be part of a plasmid, virus, ornucleic acid fragment. Typically, the expression vector includes anucleic acid to be transcribed operably linked to a promoter.

The phrase “specifically (or selectively) binds to an antibody” or“specifically (or selectively) immunoreactive with”, when referring to aprotein or peptide, refers to a binding reaction which is determinativeof the presence of the protein in the presence of a heterogeneouspopulation of proteins and other biologics. Thus, under designatedimmunoassay conditions, the specified antibodies bind to a particularprotein and do not bind in a significant amount to other proteinspresent in the sample. Specific binding to an antibody under suchconditions may require an antibody that is selected for its specificityfor a particular protein. For example, antibodies raised against aprotein having an amino acid sequence encoded by any of thepolynucleotides of the invention can be selected to obtain antibodiesspecifically immunoreactive with that protein and not with otherproteins, except for polymorphic variants. A variety of immunoassayformats may be used to select antibodies specifically immunoreactivewith a particular protein. For example, solid-phase ELISA immunoassays,Western blots, or immunohistochemistry are routinely used to selectmonoclonal antibodies specifically immunoreactive with a protein. See,Harlow and Lane Antibodies, A Laboratory Manual, Cold Spring HarborPublications, NY (1988) for a description of immunoassay formats andconditions that can be used to determine specific immunoreactivity.Typically, a specific or selective reaction will be at least twice thebackground signal or noise and more typically more than 10 to 100 timesbackground.

One who is “predisposed for a mental disorder” as used herein means aperson who has an inclination or a higher likelihood of developing amental disorder when compared to an average person in the generalpopulation.

DETAILED DESCRIPTION OF THE INVENTION

I. Introduction

To understand the genetic basis of mental disorders, studies have beenconducted to investigate the expression patterns of genes that aredifferentially expressed specifically in central nervous system ofsubjects with mood disorders. Differential and unique expression ofknown and novel genes was determined by way of interrogating total RNAsamples purified from postmortem brains of BP and MDD patients withAffymetrix Gene Chips® (containing high-density oligonucleotide probeset arrays). The fundamental principles is that by identifying genes andpathways that are differentially expressed in BP and/or MDD (relative tohealthy control subjects), via global expression profiling of thetranscriptomes as above, one can identify genes that cause, effect, orare associated with the disease, or that interact with drugs used totreat the disease, for use in diagnostic and therapeutic applications.

The present invention therefore demonstrates the altered expression(either higher or lower expression as indicated herein) and in somecases unique differential expression of the genes of Tables 3-10 at themRNA level in selected brain regions of patients diagnosed with mooddisorders, as well as the PSPHL gene (see, e.g., FIG. 14) (e.g., bipolardisorder and major depression disorder) in comparison with normalindividuals. This invention thus provides methods for diagnosis ofmental disorders such as mood disorders (e.g., bipolar disorder, majordepression, and the like) and other mental disorders having a geneticcomponent by detecting the level of a transcript or translation productof the genes listed in Tables 3-10 and FIG. 14 as well as theircorresponding biochemical pathways.

In one embodiment, the present invention relates to a novelinsertion-deletion polymorphism of phosphoserine phosphatase-like gene,and the association between deletion allele of PSPHL and susceptibilityto bipolar disorder (BPD). The fact that PSPHL shows dichotomouspresent/absent pattern of expression among individuals with brain-wideconsistency suggests genetic variation in its regulation (see Example2). Most intriguingly, we have identified an insertion/deletionpolymorphism at the PSPHL locus. The deleted genomic region spans morethan 30 kb, including the promoter region and the exons 1, 2 and 3 ofPSPHL gene. This genetic variance explains the present/absent pattern ofthe PSPHL expression. An over-representation of the deletion alleleresulting in the absence of PSPHL expression increases susceptibility toBPD. The invention therefore provides the first evidence linking agenetic variant of the PSPHL gene to bipolar disorder. The finding willfacilitate characterization of the physiological and pathologicalfunction of the gene relevant to bipolar disorder, and provides noveland significant use of this gene and its variants for diagnosis,treatment and prevention of bipolar disorder.

The invention further provides methods of identifying a compound usefulfor the treatment of such disorders by selecting compounds thatmodulates the functional effect of the translation products or theexpression of the transcripts described herein. The invention alsoprovides for methods of treating patients with such mental disorders,e.g., by administering the compounds of the invention or by genetherapy.

The genes and the polypeptides that they encode, which are associatedwith mood disorders such as bipolar disease and major depression, areuseful for facilitating the design and development of various moleculardiagnostic tools such as GeneChips™ containing probe sets specific forall or selected mental disorders, including but not limited to mooddisorders, and as an ante-and/or post-natal diagnostic tool forscreening newborns in concert with genetic counseling. Other diagnosticapplications include evaluation of disease susceptibility, prognosis,and monitoring of disease or treatment process, as well as providingindividualized medicine via predictive drug profiling systems, e.g., bycorrelating specific genomic motifs with the clinical response of apatient to individual drugs. In addition, the present invention isuseful for multiplex SNP and haplotype profiling, including but notlimited to the identification of therapeutic, diagnostic, andpharmacogenetic targets at the gene, mRNA, protein, and pathway level.Profiling of splice variants and deletions is also useful for diagnosticand therapeutic applications.

The genes and the polypeptides that they encode, described herein, arealso useful as drug targets for the development of therapeutic drugs forthe treatment or prevention of mental disorders, including but notlimited to mood disorders.

Antidepressants belong to different classes, e.g., desipramine,bupropion, and fluoxetine are in general equally effective for thetreatment of clinical depression, but act by different mechanisms. Thesimilar effectiveness of the drugs for treatment of mood disorderssuggests that they act through a presently unidentified common pathway.Animal models of depression, including treatment of animals with knowntherapeutics such as SSRIs, can be used to examine the mode of action ofthe genes of the invention. Lithium is drug of choice for treating BP.

The genes and the polypeptides that they encode, described herein, asalso useful as drug targets for the development of therapeutic drugs forthe treatment or prevention of mental disorders, including but notlimited to mood disorders. Mental disorders have a high co-morbiditywith other neurological disorders, such as Parkinson's disease orAlzheimer's. Therefore, the present invention can be used for diagnosisand treatment of patients with multiple disease states that include amental disorder such as a mood disorder. These mood disorders includeBP, MDD, and other disorders such as psychotic-depression, depressionand anxiety features, melancholic depression, chronic depression, BPIand BPII.

II. General Recombinant Nucleic Acid Methods for Use with the Invention

In numerous embodiments of the present invention, polynucleotides of theinvention will be isolated and cloned using recombinant methods. Suchpolynucleotides include, e.g., those listed in Tables 3-10 and FIG. 14,which can be used for, e.g., protein expression or during the generationof variants, derivatives, expression cassettes, to monitor geneexpression, for the isolation or detection of sequences of the inventionin different species, for diagnostic purposes in a patient, e.g., todetect mutations or to detect expression levels of nucleic acids orpolypeptides of the invention. In some embodiments, the sequences of theinvention are operably linked to a heterologous promoter. In oneembodiment, the nucleic acids of the invention are from any mammal,including, in particular, e.g., a human, a mouse, a rat, a primate, etc.

A. General Recombinant Nucleic Acids Methods

This invention relies on routine techniques in the field of recombinantgenetics. Basic texts disclosing the general methods of use in thisinvention include Sambrook et al., Molecular Cloning, A LaboratoryManual (3rd ed. 2001); Kriegler, Gene Transfer and Expression: ALaboratory Manual (1990); and Current Protocols in Molecular Biology(Ausubel et al., eds., 1994)).

For nucleic acids, sizes are given in either kilobases (kb) or basepairs (bp). These are estimates derived from agarose or acrylamide gelelectrophoresis, from sequenced nucleic acids, or from published DNAsequences. For proteins, sizes are given in kilodaltons (kDa) or aminoacid residue numbers. Proteins sizes are estimated from gelelectrophoresis, from sequenced proteins, from derived amino acidsequences, or from published protein sequences.

Oligonucleotides that are not commercially available can be chemicallysynthesized according to the solid phase phosphoramidite triester methodfirst described by Beaucage & Caruthers, Tetrahedron Letts. 22:1859-1862(1981), using an automated synthesizer, as described in Van Devanter et.al., Nucleic Acids Res. 12:6159-6168 (1984). Purification ofoligonucleotides is by either native acrylamide gel electrophoresis orby anion-exchange HPLC as described in Pearson & Reanier, J. Chrom.255:137-149 (1983).

The sequence of the cloned genes and synthetic oligonucleotides can beverified after cloning using, e.g., the chain termination method forsequencing double-stranded templates of Wallace et al., Gene 16:21-26(1981).

B. Cloning Methods for the Isolation of Nucleotide Sequences EncodingDesired Proteins

In general, the nucleic acids encoding the subject proteins are clonedfrom DNA sequence libraries that are made to encode cDNA or genomic DNA.The particular sequences can be located by hybridizing with anoligonucleotide probe, the sequence of which can be derived from thesequences of the genes listed in Tables 3-10 and FIG. 14, which providea reference for PCR primers and defines suitable regions for isolatingspecific probes. Alternatively, where the sequence is cloned into anexpression library, the expressed recombinant protein can be detectedimmunologically with antisera or purified antibodies made against apolypeptide comprising an amino acid sequence encoded by a gene listedin Table 1-8.

Methods for making and screening genomic and cDNA libraries are wellknown to those of skill in the art (see, e.g., Gubler and Hoffman Gene25:263-269 (1983); Benton and Davis Science, 196:180-182 (1977); andSambrook, supra). Brain cells are an example of suitable cells toisolate RNA and cDNA sequences of the invention.

Briefly, to make the cDNA library, one should choose a source that isrich in mRNA. The mRNA can then be made into cDNA, ligated into arecombinant vector, and transfected into a recombinant host forpropagation, screening and cloning. For a genomic library, the DNA isextracted from a suitable tissue and either mechanically sheared orenzymatically digested to yield fragments of preferably about 5-100 kb.The fragments are then separated by gradient centrifugation fromundesired sizes and are constructed in bacteriophage lambda vectors.These vectors and phage are packaged in vitro, and the recombinantphages are analyzed by plaque hybridization. Colony hybridization iscarried out as generally described in Grunstein et al., Proc. Natl.Acad. Sci. USA., 72:3961-3965 (1975).

An alternative method combines the use of synthetic oligonucleotideprimers with polymerase extension on an mRNA or DNA template. Suitableprimers can be designed from specific sequences of the invention. Thispolymerase chain reaction (PCR) method amplifies the nucleic acidsencoding the protein of interest directly from mRNA, cDNA, genomiclibraries or cDNA libraries. Restriction endonuclease sites can beincorporated into the primers. Polymerase chain reaction or other invitro amplification methods may also be useful, for example, to clonenucleic acids encoding specific proteins and express said proteins, tosynthesize nucleic acids that will be used as probes for detecting thepresence of mRNA encoding a polypeptide of the invention inphysiological samples, for nucleic acid sequencing, or for otherpurposes (see, U.S. Pat. Nos. 4,683,195 and 4,683,202). Genes amplifiedby a PCR reaction can be purified from agarose gels and cloned into anappropriate vector.

Appropriate primers and probes for identifying polynucleotides of theinvention from mammalian tissues can be derived from the sequencesprovided herein. For a general overview of PCR, see, Innis et al. PCRProtocols: A Guide to Methods and Applications, Academic Press, SanDiego (1990).

Synthetic oligonucleotides can be used to construct genes. This is doneusing a series of overlapping oligonucleotides, usually 40-120 bp inlength, representing both the sense and anti-sense strands of the gene.These DNA fragments are then annealed, ligated and cloned.

A gene encoding a polypeptide of the invention can be cloned usingintermediate vectors before transformation into mammalian cells forexpression. These intermediate vectors are typically prokaryote vectorsor shuttle vectors. The proteins can be expressed in either prokaryotes,using standard methods well known to those of skill in the art, oreukaryotes as described infra.

III. Purification of Proteins of the Invention

Either naturally occurring or recombinant polypeptides of the inventioncan be purified for use in functional assays. Naturally occurringpolypeptides, e.g., polypeptides encoded by genes listed in Tables 3-10and FIG. 14, can be purified, for example, from mouse or human tissuesuch as brain or any other source of an ortholog. Recombinantpolypeptides can be purified from any suitable expression system.

The polypeptides of the invention may be purified to substantial purityby standard techniques, including selective precipitation with suchsubstances as ammonium sulfate; column chromatography,immunopurification methods, and others (see, e.g., Scopes, ProteinPurification: Principles and Practice (1982); U.S. Pat. No. 4,673,641;Ausubel et al., supra; and Sambrook et al., supra).

A number of procedures can be employed when recombinant polypeptides arepurified. For example, proteins having established molecular adhesionproperties can be reversible fused to polypeptides of the invention.With the appropriate ligand, the polypeptides can be selectivelyadsorbed to a purification column and then freed from the column in arelatively pure form. The fused protein is then removed by enzymaticactivity. Finally the polypeptide can be purified using immunoaffinitycolumns.

A. Purification of Proteins from Recombinant Bacteria

When recombinant proteins are expressed by the transformed bacteria inlarge amounts, typically after promoter induction, although expressioncan be constitutive, the proteins may form insoluble aggregates. Thereare several protocols that are suitable for purification of proteininclusion bodies. For example, purification of aggregate proteins(hereinafter referred to as inclusion bodies) typically involves theextraction, separation and/or purification of inclusion bodies bydisruption of bacterial cells typically, but not limited to, byincubation in a buffer of about 100-150 μg/ml lysozyme and 0.1% NonidetP40, a non-ionic detergent. The cell suspension can be ground using aPolytron grinder (Brinkman Instruments, Westbury, N.Y.). Alternatively,the cells can be sonicated on ice. Alternate methods of lysing bacteriaare described in Ausubel et al. and Sambrook et al., both supra, andwill be apparent to those of skill in the art.

The cell suspension is generally centrifuged and the pellet containingthe inclusion bodies resuspended in buffer which does not dissolve butwashes the inclusion bodies, e.g., 20 mM Tris-HCl (pH 7.2), 1 mM EDTA,150 mM NaCl and 2% Triton-X 100, a non-ionic detergent. It may benecessary to repeat the wash step to remove as much cellular debris aspossible. The remaining pellet of inclusion bodies may be resuspended inan appropriate buffer (e.g., 20 mM sodium phosphate, pH 6.8, 150 mMNaCl). Other appropriate buffers will be apparent to those of skill inthe art.

Following the washing step, the inclusion bodies are solubilized by theaddition of a solvent that is both a strong hydrogen acceptor and astrong hydrogen donor (or a combination of solvents each having one ofthese properties). The proteins that formed the inclusion bodies maythen be renatured by dilution or dialysis with a compatible buffer.Suitable solvents include, but are not limited to, urea (from about 4 Mto about 8 M), formamide (at least about 80%, volume/volume basis), andguanidine hydrochloride (from about 4 M to about 8 M). Some solventsthat are capable of solubilizing aggregate-forming proteins, such as SDS(sodium dodecyl sulfate) and 70% formic acid, are inappropriate for usein this procedure due to the possibility of irreversible denaturation ofthe proteins, accompanied by a lack of immunogenicity and/or activity.Although guanidine hydrochloride and similar agents are denaturants,this denaturation is not irreversible and renaturation may occur uponremoval (by dialysis, for example) or dilution of the denaturant,allowing re-formation of the immunologically and/or biologically activeprotein of interest. After solubilization, the protein can be separatedfrom other bacterial proteins by standard separation techniques.

Alternatively, it is possible to purify proteins from bacteriaperiplasm. Where the protein is exported into the periplasm of thebacteria, the periplasmic fraction of the bacteria can be isolated bycold osmotic shock in addition to other methods known to those of skillin the art (see, Ausubel et al., supra). To isolate recombinant proteinsfrom the periplasm, the bacterial cells are centrifuged to form apellet. The pellet is resuspended in a buffer containing 20% sucrose. Tolyse the cells, the bacteria are centrifuged and the pellet isresuspended in ice-cold 5 mM MgSO₄ and kept in an ice bath forapproximately 10 minutes. The cell suspension is centrifuged and thesupernatant decanted and saved. The recombinant proteins present in thesupernatant can be separated from the host proteins by standardseparation techniques well known to those of skill in the art.

B. Standard Protein Separation Techniques for Purifying Proteins

1. Solubility Fractionation

Often as an initial step, and if the protein mixture is complex, aninitial salt fractionation can separate many of the unwanted host cellproteins (or proteins derived from the cell culture media) from therecombinant protein of interest. The preferred salt is ammonium sulfate.Ammonium sulfate precipitates proteins by effectively reducing theamount of water in the protein mixture. Proteins then precipitate on thebasis of their solubility. The more hydrophobic a protein is, the morelikely it is to precipitate at lower ammonium sulfate concentrations. Atypical protocol is to add saturated ammonium sulfate to a proteinsolution so that the resultant ammonium sulfate concentration is between20-30%. This will precipitate the most hydrophobic proteins. Theprecipitate is discarded (unless the protein of interest is hydrophobic)and ammonium sulfate is added to the supernatant to a concentrationknown to precipitate the protein of interest. The precipitate is thensolubilized in buffer and the excess salt removed if necessary, througheither dialysis or diafiltration. Other methods that rely on solubilityof proteins, such as cold ethanol precipitation, are well known to thoseof skill in the art and can be used to fractionate complex proteinmixtures.

2. Size Differential Filtration

Based on a calculated molecular weight, a protein of greater and lessersize can be isolated using ultrafiltration through membranes ofdifferent pore sizes (for example, Amicon or Millipore membranes). As afirst step, the protein mixture is ultrafiltered through a membrane witha pore size that has a lower molecular weight cut-off than the molecularweight of the protein of interest. The retentate of the ultrafiltrationis then ultrafiltered against a membrane with a molecular cut offgreater than the molecular weight of the protein of interest. Therecombinant protein will pass through the membrane into the filtrate.The filtrate can then be chromatographed as described below.

3. Column Chromatography

The proteins of interest can also be separated from other proteins onthe basis of their size, net surface charge, hydrophobicity and affinityfor ligands. In addition, antibodies raised against proteins can beconjugated to column matrices and the proteins immunopurified. All ofthese methods are well known in the art.

It will be apparent to one of skill that chromatographic techniques canbe performed at any scale and using equipment from many differentmanufacturers (e.g., Pharmacia Biotech).

IV. Detection of Gene Expression

Those of skill in the art will recognize that detection of expression ofpolynucleotides of the invention has many uses. For example, asdiscussed herein, detection of the level of polypeptides orpolynucleotides of the invention in a patient is useful for diagnosingmood disorders or psychotic disorders or a predisposition for a mooddisorder or psychotic disorders. Moreover, detection of gene expressionis useful to identify modulators of expression of the polypeptides orpolynucleotides of the invention.

A variety of methods of specific DNA and RNA measurement using nucleicacid hybridization techniques are known to those of skill in the art(see, Sambrook, supra). Some methods involve an electrophoreticseparation (e.g., Southern blot for detecting DNA, and Northern blot fordetecting RNA), but measurement of DNA and RNA can also be carried outin the absence of electrophoretic separation (e.g., by dot blot).Southern blot of genomic DNA (e.g., from a human) can be used forscreening for restriction fragment length polymorphism (RFLP) to detectthe presence of a genetic disorder affecting a polypeptide of theinvention.

The selection of a nucleic acid hybridization format is not critical. Avariety of nucleic acid hybridization formats are known to those skilledin the art. For example, common formats include sandwich assays andcompetition or displacement assays. Hybridization techniques aregenerally described in Hames and Higgins Nucleic Acid Hybridization, APractical Approach, IRL Press (1985); Gall and Pardue, Proc. Natl. Acad.Sci. U.S.A., 63:378-383 (1969); and John et al. Nature, 223:582-587(1969).

Detection of a hybridization complex may require the binding of asignal-generating complex to a duplex of target and probepolynucleotides or nucleic acids. Typically, such binding occurs throughligand and anti-ligand interactions as between a ligand-conjugated probeand an anti-ligand conjugated with a signal. The binding of the signalgeneration complex is also readily amenable to accelerations by exposureto ultrasonic energy.

The label may also allow indirect detection of the hybridizationcomplex. For example, where the label is a hapten or antigen, the samplecan be detected by using antibodies. In these systems, a signal isgenerated by attaching fluorescent or enzyme molecules to the antibodiesor in some cases, by attachment to a radioactive label (see, e.g.,Tijssen, “Practice and Theory of Enzyme Immunoassays,” LaboratoryTechniques in Biochemistry and Molecular Biology, Burdon and vanKnippenberg Eds., Elsevier (1985), pp. 9-20).

The probes are typically labeled either directly, as with isotopes,chromophores, lumiphores, chromogens, or indirectly, such as withbiotin, to which a streptavidin complex may later bind. Thus, thedetectable labels used in the assays of the present invention can beprimary labels (where the label comprises an element that is detecteddirectly or that produces a directly detectable element) or secondarylabels (where the detected label binds to a primary label, e.g., as iscommon in immunological labeling). Typically, labeled signal nucleicacids are used to detect hybridization. Complementary nucleic acids orsignal nucleic acids may be labeled by any one of several methodstypically used to detect the presence of hybridized polynucleotides. Themost common method of detection is the use of autoradiography with ³H,^(125l I,) ³⁵S, ¹⁴C, or ³²P-labeled probes or the like.

Other labels include, e.g., ligands that bind to labeled antibodies,fluorophores, chemiluminescent agents, enzymes, and antibodies which canserve as specific binding pair members for a labeled ligand. Anintroduction to labels, labeling procedures and detection of labels isfound in Polak and Van Noorden Introduction to Immunocytochemistry, 2nded., Springer Verlag, NY (1997); and in Haugland Handbook of FluorescentProbes and Research Chemicals, a combined handbook and cataloguePublished by Molecular Probes, Inc. (1996).

In general, a detector which monitors a particular probe or probecombination is used to detect the detection reagent label. Typicaldetectors include spectrophotometers, phototubes and photodiodes,microscopes, scintillation counters, cameras, film and the like, as wellas combinations thereof. Examples of suitable detectors are widelyavailable from a variety of commercial sources known to persons of skillin the art. Commonly, an optical image of a substrate comprising boundlabeling moieties is digitized for subsequent computer analysis.

Most typically, the amount of RNA is measured by quantifying the amountof label fixed to the solid support by binding of the detection reagent.Typically, the presence of a modulator during incubation will increaseor decrease the amount of label fixed to the solid support relative to acontrol incubation which does not comprise the modulator, or as comparedto a baseline established for a particular reaction type. Means ofdetecting and quantifying labels are well known to those of skill in theart.

In preferred embodiments, the target nucleic acid or the probe isimmobilized on a solid support. Solid supports suitable for use in theassays of the invention are known to those of skill in the art. As usedherein, a solid support is a matrix of material in a substantially fixedarrangement.

A variety of automated solid-phase assay techniques are alsoappropriate. For instance, very large scale immobilized polymer arrays(VLSIPS™), available from Affymetrix, Inc. (Santa Clara, Calif.) can beused to detect changes in expression levels of a plurality of genesinvolved in the same regulatory pathways simultaneously. See, Tijssen,supra., Fodor et al. (1991) Science, 251: 767-777; Sheldon et al. (1993)Clinical Chemistry 39(4): 718-719, and Kozal et al. (1996) NatureMedicine 2(7): 753-759.

Detection can be accomplished, for example, by using a labeled detectionmoiety that binds specifically to duplex nucleic acids (e.g., anantibody that is specific for RNA-DNA duplexes). One preferred exampleuses an antibody that recognizes DNA-RNA heteroduplexes in which theantibody is linked to an enzyme (typically by recombinant or covalentchemical bonding). The antibody is detected when the enzyme reacts withits substrate, producing a detectable product. Coutlee et al. (1989)Analytical Biochemistry 181:153-162; Bogulavski (1986) et al. J.Immunol. Methods 89:123-130; Prooijen-Knegt (1982) Exp. Cell Res.141:397-407; Rudkin (1976) Nature 265:472-473, Stollar (1970) Proc.Nat'l Acad. Sci. USA 65:993-1000; Ballard (1982) Mol. Immunol.19:793-799; Pisetsky and Caster (1982) Mol. Immunol. 19:645-650; Viscidiet al. (1988) J. Clin. Microbial. 41:199-209; and Kiney et al. (1989) J.Clin. Microbiol. 27:6-12 describe antibodies to RNA duplexes, includinghomo and heteroduplexes. Kits comprising antibodies specific for DNA:RNAhybrids are available, e.g., from Digene Diagnostics, Inc. (Beltsville,Md.).

In addition to available antibodies, one of skill in the art can easilymake antibodies specific for nucleic acid duplexes using existingtechniques, or modify those antibodies that are commercially or publiclyavailable. In addition to the art referenced above, general methods forproducing polyclonal and monoclonal antibodies are known to those ofskill in the art (see, e.g., Paul (3rd ed.) Fundamental Immunology RavenPress, Ltd., NY (1993); Coligan Current Protocols in ImmunologyWiley/Greene, NY (1991); Harlow and Lane Antibodies: A Laboratory ManualCold Spring Harbor Press, NY (1988); Stites et al. (eds.) Basic andClinical Immunology (4th ed.) Lange Medical Publications, Los Altos,Calif., and references cited therein; Goding Monoclonal Antibodies:Principles and Practice (2d ed.) Academic Press, New York, N.Y., (1986);and Kohler and Milstein Nature 256: 495-497 (1975)). Other suitabletechniques for antibody preparation include selection of libraries ofrecombinant antibodies in phage or similar vectors (see, Huse et al.Science 246:1275-1281 (1989); and Ward et al. Nature 341:544-546(1989)). Specific monoclonal and polyclonal antibodies and antisera willusually bind with a K_(D) of at least about 0.1 μM, preferably at leastabout 0.01 μM or better, and most typically and preferably, 0.001 μM orbetter.

The nucleic acids used in this invention can be either positive ornegative probes. Positive probes bind to their targets and the presenceof duplex formation is evidence of the presence of the target. Negativeprobes fail to bind to the suspect target and the absence of duplexformation is evidence of the presence of the target. For example, theuse of a wild type specific nucleic acid probe or PCR primers may serveas a negative probe in an assay sample where only the nucleotidesequence of interest is present.

The sensitivity of the hybridization assays may be enhanced through useof a nucleic acid amplification system that multiplies the targetnucleic acid being detected. Examples of such systems include thepolymerase chain reaction (PCR) system, in particular RT-PCR or realtime PCR, and the ligase chain reaction (LCR) system. Other methodsrecently described in the art are the nucleic acid sequence basedamplification (NASBA, Cangene, Mississauga, Ontario) and Q BetaReplicase systems. These systems can be used to directly identifymutants where the PCR or LCR primers are designed to be extended orligated only when a selected sequence is present. Alternatively, theselected sequences can be generally amplified using, for example,nonspecific PCR primers and the amplified target region later probed fora specific sequence indicative of a mutation.

An alternative means for determining the level of expression of thenucleic acids of the present invention is in situ hybridization. In situhybridization assays are well known and are generally described inAngerer et al., Methods Enzymol. 152:649-660 (1987). In an in situhybridization assay, cells, preferentially human cells from thecerebellum or the hippocampus, are fixed to a solid support, typically aglass slide. If DNA is to be probed, the cells are denatured with heator alkali. The cells are then contacted with a hybridization solution ata moderate temperature to permit annealing of specific probes that arelabeled. The probes are preferably labeled with radioisotopes orfluorescent reporters.

V. Immunological Detection of the Polypeptides of the Invention

In addition to the detection of polynucleotide expression using nucleicacid hybridization technology, one can also use immunoassays to detectpolypeptides of the invention. Immunoassays can be used to qualitativelyor quantitatively analyze polypeptides. A general overview of theapplicable technology can be found in Harlow & Lane, Antibodies: ALaboratory Manual (1988).

A. Antibodies to Target Polypeptides or Other Immunogens

Methods for producing polyclonal and monoclonal antibodies that reactspecifically with a protein of interest or other immunogen are known tothose of skill in the art (see, e.g., Coligan, supra; and Harlow andLane, supra; Stites et al., supra and references cited therein; Goding,supra; and Kohler and Milstein Nature, 256:495-497 (1975)). Suchtechniques include antibody preparation by selection of antibodies fromlibraries of recombinant antibodies in phage or similar vectors (see,Huse et al., supra; and Ward et al., supra). For example, in order toproduce antisera for use in an immunoassay, the protein of interest oran antigenic fragment thereof, is isolated as described herein. Forexample, a recombinant protein is produced in a transformed cell line.An inbred strain of mice or rabbits is immunized with the protein usinga standard adjuvant, such as Freund's adjuvant, and a standardimmunization protocol. Alternatively, a synthetic peptide derived fromthe sequences disclosed herein and conjugated to a carrier protein canbe used as an immunogen.

Polyclonal sera are collected and titered against the immunogen in animmunoassay, for example, a solid phase immunoassay with the immunogenimmobilized on a solid support. Polyclonal antisera with a titer of 10⁴or greater are selected and tested for their cross-reactivity againstunrelated proteins or even other homologous proteins from otherorganisms, using a competitive binding immunoassay. Specific monoclonaland polyclonal antibodies and antisera will usually bind with a K_(D) ofat least about 0.1 mM, more usually at least about 1 μM, preferably atleast about 0.1 μM or better, and most preferably, 0.01 μM or better.

A number of proteins of the invention comprising immunogens may be usedto produce antibodies specifically or selectively reactive with theproteins of interest. Recombinant protein is the preferred immunogen forthe production of monoclonal or polyclonal antibodies. Naturallyoccurring protein, such as one comprising an amino acid sequence encodedby a gene listed in Table 1-8 may also be used either in pure or impureform. Synthetic peptides made using the protein sequences describedherein may also be used as an immunogen for the production of antibodiesto the protein. Recombinant protein can be expressed in eukaryotic orprokaryotic cells and purified as generally described supra. The productis then injected into an animal capable of producing antibodies. Eithermonoclonal or polyclonal antibodies may be generated for subsequent usein immunoassays to measure the protein.

Methods of production of polyclonal antibodies are known to those ofskill in the art. In brief, an immunogen, preferably a purified protein,is mixed with an adjuvant and animals are immunized. The animal's immuneresponse to the immunogen preparation is monitored by taking test bleedsand determining the titer of reactivity to the polypeptide of interest.When appropriately high titers of antibody to the immunogen areobtained, blood is collected from the animal and antisera are prepared.Further fractionation of the antisera to enrich for antibodies reactiveto the protein can be done if desired (see, Harlow and Lane, supra).

Monoclonal antibodies may be obtained using various techniques familiarto those of skill in the art. Typically, spleen cells from an animalimmunized with a desired antigen are immortalized, commonly by fusionwith a myeloma cell (see, Kohler and Milstein, Eur. J. Immunol.6:511-519 (1976)). Alternative methods of immortalization include, e.g.,transformation with Epstein Barr Virus, oncogenes, or retroviruses, orother methods well known in the art. Colonies arising from singleimmortalized cells are screened for production of antibodies of thedesired specificity and affinity for the antigen, and yield of themonoclonal antibodies produced by such cells may be enhanced by varioustechniques, including injection into the peritoneal cavity of avertebrate host. Alternatively, one may isolate DNA sequences whichencode a monoclonal antibody or a binding fragment thereof by screeninga DNA library from human B cells according to the general protocoloutlined by Huse et al., supra.

Once target protein specific antibodies are available, the protein canbe measured by a variety of immunoassay methods with qualitative andquantitative results available to the clinician. For a review ofimmunological and immunoassay procedures in general see, Stites, supra.Moreover, the immunoassays of the present invention can be performed inany of several configurations, which are reviewed extensively in MaggioEnzyme Immunoassay, CRC Press, Boca Raton, Fla. (1980); Tijssen, supra;and Harlow and Lane, supra.

Immunoassays to measure target proteins in a human sample may use apolyclonal antiserum that was raised to the protein (e.g., one has anamino acid sequence encoded by a gene listed in Table 1-8) or a fragmentthereof. This antiserum is selected to have low cross-reactivity againstdifferent proteins and any such cross-reactivity is removed byimmunoabsorption prior to use in the immunoassay.

B. Immunological Binding Assays

In a preferred embodiment, a protein of interest is detected and/orquantified using any of a number of well-known immunological bindingassays (see, e.g., U.S. Pat. Nos. 4,366,241; 4,376,110; 4,517,288; and4,837,168). For a review of the general immunoassays, see also AsaiMethods in Cell Biology Volume 37: Antibodies in Cell Biology, AcademicPress, Inc. NY (1993); Stites, supra. Immunological binding assays (orimmunoassays) typically utilize a “capture agent” to specifically bindto and often immobilize the analyte (in this case a polypeptide of thepresent invention or antigenic subsequences thereof). The capture agentis a moiety that specifically binds to the analyte. In a preferredembodiment, the capture agent is an antibody that specifically binds,for example, a polypeptide of the invention. The antibody may beproduced by any of a number of means well known to those of skill in theart and as described above.

Immunoassays also often utilize a labeling agent to specifically bind toand label the binding complex formed by the capture agent and theanalyte. The labeling agent may itself be one of the moieties comprisingthe antibody/analyte complex. Alternatively, the labeling agent may be athird moiety, such as another antibody, that specifically binds to theantibody/protein complex.

In a preferred embodiment, the labeling agent is a second antibodybearing a label. Alternatively, the second antibody may lack a label,but it may, in turn, be bound by a labeled third antibody specific toantibodies of the species from which the second antibody is derived. Thesecond antibody can be modified with a detectable moiety, such asbiotin, to which a third labeled molecule can specifically bind, such asenzyme-labeled streptavidin.

Other proteins capable of specifically binding immunoglobulin constantregions, such as protein A or protein G, can also be used as the labelagents. These proteins are normal constituents of the cell walls ofstreptococcal bacteria. They exhibit a strong non-immunogenic reactivitywith immunoglobulin constant regions from a variety of species (see,generally, Kronval, et al. J. Immunol., 111: 1401-1406 (1973); andAkerstrom, et al. J. Immunol., 135:2589-2542 (1985)).

Throughout the assays, incubation and/or washing steps may be requiredafter each combination of reagents. Incubation steps can vary from about5 seconds to several hours, preferably from about 5 minutes to about 24hours. The incubation time will depend upon the assay format, analyte,volume of solution, concentrations, and the like. Usually, the assayswill be carried out at ambient temperature, although they can beconducted over a range of temperatures, such as 10° C. to 40° C.

1. Non-Competitive Assay Formats

Immunoassays for detecting proteins of interest from tissue samples maybe either competitive or noncompetitive. Noncompetitive immunoassays areassays in which the amount of captured analyte (in this case theprotein) is directly measured. In one preferred “sandwich” assay, forexample, the capture agent (e.g., antibodies specific for a polypeptideencoded by a gene listed in Table 1-8) can be bound directly to a solidsubstrate where it is immobilized. These immobilized antibodies thencapture the polypeptide present in the test sample. The polypeptide thusimmobilized is then bound by a labeling agent, such as a second antibodybearing a label. Alternatively, the second antibody may lack a label,but it may, in turn, be bound by a labeled third antibody specific toantibodies of the species from which the second antibody is derived. Thesecond can be modified with a detectable moiety, such as biotin, towhich a third labeled molecule can specifically bind, such asenzyme-labeled streptavidin.

2. Competitive Assay Formats

In competitive assays, the amount of analyte (such as a polypeptideencoded by a gene listed in Table 1-8) present in the sample is measuredindirectly by measuring the amount of an added (exogenous) analytedisplaced (or competed away) from a capture agent (e.g., an antibodyspecific for the analyte) by the analyte present in the sample. In onecompetitive assay, a known amount of, in this case, the protein ofinterest is added to the sample and the sample is then contacted with acapture agent, in this case an antibody that specifically binds to apolypeptide of the invention. The amount of immunogen bound to theantibody is inversely proportional to the concentration of immunogenpresent in the sample. In a particularly preferred embodiment, theantibody is immobilized on a solid substrate. For example, the amount ofthe polypeptide bound to the antibody may be determined either bymeasuring the amount of subject protein present in a protein/antibodycomplex or, alternatively, by measuring the amount of remaininguncomplexed protein. The amount of protein may be detected by providinga labeled protein molecule.

Immunoassays in the competitive binding format can be used forcross-reactivity determinations. For example, a protein of interest canbe immobilized on a solid support. Proteins are added to the assay whichcompete with the binding of the antisera to the immobilized antigen. Theability of the above proteins to compete with the binding of theantisera to the immobilized protein is compared to that of the proteinof interest. The percent cross-reactivity for the above proteins iscalculated, using standard calculations. Those antisera with less than10% cross-reactivity with each of the proteins listed above are selectedand pooled. The cross-reacting antibodies are optionally removed fromthe pooled antisera by immunoabsorption with the considered proteins,e.g., distantly related homologs.

The immunoabsorbed and pooled antisera are then used in a competitivebinding immunoassay as described above to compare a second protein,thought to be perhaps a protein of the present invention, to theimmunogen protein. In order to make this comparison, the two proteinsare each assayed at a wide range of concentrations and the amount ofeach protein required to inhibit 50% of the binding of the antisera tothe immobilized protein is determined. If the amount of the secondprotein required is less than 10 times the amount of the proteinpartially encoded by a sequence herein that is required, then the secondprotein is said to specifically bind to an antibody generated to animmunogen consisting of the target protein.

3. Other Assay Formats

In a particularly preferred embodiment, western blot (immunoblot)analysis is used to detect and quantify the presence of a polypeptide ofthe invention in the sample. The technique generally comprisesseparating sample proteins by gel electrophoresis on the basis ofmolecular weight, transferring the separated proteins to a suitablesolid support (such as, e.g., a nitrocellulose filter, a nylon filter,or a derivatized nylon filter) and incubating the sample with theantibodies that specifically bind the protein of interest. For example,the antibodies specifically bind to a polypeptide of interest on thesolid support. These antibodies may be directly labeled or alternativelymay be subsequently detected using labeled antibodies (e.g., labeledsheep anti-mouse antibodies) that specifically bind to the antibodiesagainst the protein of interest.

Other assay formats include liposome immunoassays (LIA), which useliposomes designed to bind specific molecules (e.g., antibodies) andrelease encapsulated reagents or markers. The released chemicals arethen detected according to standard techniques (see, Monroe et al.(1986) Amer. Clin. Prod. Rev. 5:34-41).

4. Labels

The particular label or detectable group used in the assay is not acritical aspect of the invention, as long as it does not significantlyinterfere with the specific binding of the antibody used in the assay.The detectable group can be any material having a detectable physical orchemical property. Such detectable labels have been well developed inthe field of immunoassays and, in general, most labels useful in suchmethods can be applied to the present invention. Thus, a label is anycomposition detectable by spectroscopic, photochemical, biochemical,immunochemical, electrical, optical or chemical means. Useful labels inthe present invention include magnetic beads (e.g., Dynabeads™),fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red,rhodamine, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or³²P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase andothers commonly used in an ELISA), and colorimetric labels such ascolloidal gold or colored glass or plastic (e.g., polystyrene,polypropylene, latex, etc.) beads.

The label may be coupled directly or indirectly to the desired componentof the assay according to methods well known in the art. As indicatedabove, a wide variety of labels may be used, with the choice of labeldepending on the sensitivity required, the ease of conjugation with thecompound, stability requirements, available instrumentation, anddisposal provisions.

Non-radioactive labels are often attached by indirect means. Themolecules can also be conjugated directly to signal generatingcompounds, e.g., by conjugation with an enzyme or fluorescent compound.A variety of enzymes and fluorescent compounds can be used with themethods of the present invention and are well-known to those of skill inthe art (for a review of various labeling or signal producing systemswhich may be used, see, e.g., U.S. Pat. No. 4,391,904).

Means of detecting labels are well known to those of skill in the art.Thus, for example, where the label is a radioactive label, means fordetection include a scintillation counter or photographic film as inautoradiography. Where the label is a fluorescent label, it may bedetected by exciting the fluorochrome with the appropriate wavelength oflight and detecting the resulting fluorescence. The fluorescence may bedetected visually, by means of photographic film, by the use ofelectronic detectors such as charge-coupled devices (CCDs) orphotomultipliers and the like. Similarly, enzymatic labels may bedetected by providing the appropriate substrates for the enzyme anddetecting the resulting reaction product. Finally simple colorimetriclabels may be detected directly by observing the color associated withthe label. Thus, in various dipstick assays, conjugated gold oftenappears pink, while various conjugated beads appear the color of thebead.

Some assay formats do not require the use of labeled components. Forinstance, agglutination assays can be used to detect the presence of thetarget antibodies. In this case, antigen-coated particles areagglutinated by samples comprising the target antibodies. In thisformat, none of the components need to be labeled and the presence ofthe target antibody is detected by simple visual inspection.

In some embodiments, BP or MDD in a patient may be diagnosed orotherwise evaluated by visualizing expression in situ of one or more ofthe appropriately dysregulated gene sequences identified herein. Thoseskilled in the art of visualizing the presence or expression ofmolecules including nucleic acids, polypeptides and other biochemicalsin the brains of living patients will appreciate that the geneexpression information described herein may be utilized in the contextof a variety of visualization methods. Such methods include, but are notlimited to, single-photon emission-computed tomography (SPECT) andpositron-emitting tomography (PET) methods. See, e.g., Vassaux andGroot-wassink, “In Vivo Noninvasive Imaging for Gene Therapy,” J.Biomedicine and Biotechnology, 2: 92-101 (2003).

PET and SPECT imaging shows the chemical functioning of organs andtissues, while other imaging techniques—such as X-ray, CT and MRI—showstructure. The use of PET and SPECT imaging is useful for qualifying andmonitoring the development of brain diseases, including schizophreniaand related disorders. In some instances, the use of PET or SPECTimaging allows diseases to be detected years earlier than the onset ofsymptoms. The use of small molecules for labelling and visualizing thepresence or expression of polypeptides and nucleotides has had success,for example, in visualizing proteins in the brains of Alzheimer'spatients, as described by, e.g., Herholz K et al., Mol Imaging Biol.,6(4):239-69 (2004); Nordberg A, Lancet Neurol., 3(9):519-27 (2004);Neuropsychol Rev., Zakzanis K K et al., 13(1):1-18 (2003); Kung M P etal, Brain Res.,1025(1-2):98-105 (2004); and Herholz K, Ann Nucl Med.,17(2):79-89 (2003).

The dysregulated genes disclosed in Tables 1-30, or their encodedpeptides (if any), or fragments thereof, can be used in the context ofPET and SPECT imaging applications. After modification with appropriatetracer residues for PET or SPECT applications, molecules which interactor bind with the transcripts in Tables 1-30 or with any polypeptidesencoded by those transcripts may be used to visualize the patterns ofgene expression and facilitate diagnosis of schizophrenia MDD or BP, asdescribed herein. Similarly, if the encoded polypeptides encode enzymes,labeled molecules which interact with the products of catalysis by theenzyme may be used for the in vivo imaging and diagnostic applicationdescribed herein.

Antisense technology is particularly suitable for detecting the thetranscripts identified in Tables 1-30 herein. For example, the use ofantisense peptide nucleic acid (PNA) labeled with an appropriateradionuclide, such as ¹¹¹In, and conjugated to a brain drug-targetingsystem to enable transport across biologic membrane barriers, has beendemonstrated to allow imaging of endogenous gene expression in braincancer. See Suzuki et al., Journal of Nuclear Medicine, 10:1766-1775(2004). Suzuki et al. utilize a delivery system comprising monoclonalantibodies that target transferring receptors at the blood-brain barrierand facilitate transport of the PNA across that barrier. Modifiedembodiments of this technique may be used to target upregulated genesassociated with schizophrenia, BP or MDD, such as the upregulated geneswhich appear in Tables 1-30, in methods of treating schizophrenic, BP orMDD patients.

In other embodiments, the dysregulated genes listed in Tables 1-30 maybe used in the context of prenatal and neonatal diagnostic methods. Forexample, fetal or neonatal samples can be obtained and the expressionlevels of appropriate transcripts (e.g., the transcripts in Table 19)may be measured and correlated with the presence or increased likelihoodof a mental disorder, e.g., MDD. Similarly, the presence of one or moreof the SNPs identified in the Tables, e.g., Table 27 may be used toinfer or corroborate dysregulated expression of a gene and thelikelihood of a mood disorder in prenatal, neonatal, children and adultpatients.

In other embodiments, the brain labeling and imaging techniquesdescribed herein or variants thereof may be used in conjunction with anyof the dysregulated gene sequences in Tables 1-30 in a forensicanalysis, i.e., to determine whether a deceased individual suffered fromschizophrenia, BP, or MDD.

VI. Screening for Modulators of Polypeptides and Polynucleotides of theInvention

Modulators of polypeptides or polynucleotides of the invention, i.e.agonists or antagonists of their activity or modulators of polypeptideor polynucleotide expression, are useful for treating a number of humandiseases, including mood disorders or psychotic disorders.Administration of agonists, antagonists or other agents that modulateexpression of the polynucleotides or polypeptides of the invention canbe used to treat patients with mood disorders or psychotic disorders.

A. Screening Methods

A number of different screening protocols can be utilized to identifyagents that modulate the level of expression or activity of polypeptidesand polynucleotides of the invention in cells, particularly mammaliancells, and especially human cells. In general terms, the screeningmethods involve screening a plurality of agents to identify an agentthat modulates the polypeptide activity by binding to a polypeptide ofthe invention, modulating inhibitor binding to the polypeptide oractivating expression of the polypeptide or polynucleotide, for example.

1. Binding Assays

Preliminary screens can be conducted by screening for agents capable ofbinding to a polypeptide of the invention, as at least some of theagents so identified are likely modulators of polypeptide activity. Thebinding assays usually involve contacting a polypeptide of the inventionwith one or more test agents and allowing sufficient time for theprotein and test agents to form a binding complex. Any binding complexesformed can be detected using any of a number of established analyticaltechniques. Protein binding assays include, but are not limited to,methods that measure co-precipitation, co-migration on non-denaturingSDS-polyacrylamide gels, and co-migration on Western blots (see, e.g.,Bennet and Yamamura, (1985) “Neurotransmitter, Hormone or Drug ReceptorBinding Methods,” in Neurotransmitter Receptor Binding (Yamamura, H. I.,et al., eds.), pp. 61-89. The protein utilized in such assays can benaturally expressed, cloned or synthesized.

Binding assays are also useful, e.g., for identifying endogenousproteins that interact with a polypeptide of the invention. For example,antibodies, receptors or other molecules that bind a polypeptide of theinvention can be identified in binding assays.

2. Expression Assays

Certain screening methods involve screening for a compound that up ordown-regulates the expression of a polypeptide or polynucleotide of theinvention. Such methods generally involve conducting cell-based assaysin which test compounds are contacted with one or more cells expressinga polypeptide or polynucleotide of the invention and then detecting anincrease or decrease in expression (either transcript, translationproduct, or catalytic product). Some assays are performed withperipheral cells, or other cells, that express an endogenous polypeptideor polynucleotide of the invention.

Polypeptide or polynucleotide expression can be detected in a number ofdifferent ways. As described infra, the expression level of apolynucleotide of the invention in a cell can be determined by probingthe mRNA expressed in a cell with a probe that specifically hybridizeswith a transcript (or complementary nucleic acid derived therefrom) of apolynucleotide of the invention. Probing can be conducted by lysing thecells and conducting Northern blots or without lysing the cells using insitu-hybridization techniques. Alternatively, a polypeptide of theinvention can be detected using immunological methods in which a celllysate is probed with antibodies that specifically bind to a polypeptideof the invention.

Other cell-based assays are reporter assays conducted with cells that donot express a polypeptide or polynucleotide of the invention. Certain ofthese assays are conducted with a heterologous nucleic acid constructthat includes a promoter of a polynucleotide of the invention that isoperably linked to a reporter gene that encodes a detectable product. Anumber of different reporter genes can be utilized. Some reporters areinherently detectable. An example of such a reporter is greenfluorescent protein that emits fluorescence that can be detected with afluorescence detector. Other reporters generate a detectable product.Often such reporters are enzymes. Exemplary enzyme reporters include,but are not limited to, 62 -glucuronidase, chloramphenicol acetyltransferase (CAT); Alton and Vapnek (1979) Nature 282:864-869),luciferase, β-galactosidase, green fluorescent protein (GFP) andalkaline phosphatase (Toh, et al. (1980) Eur. J. Biochem. 182:231-238;and Hall et al. (1983) J. Mol. Appl. Gen. 2:101).

In these assays, cells harboring the reporter construct are contactedwith a test compound. A test compound that either activates the promoterby binding to it or triggers a cascade that produces a molecule thatactivates the promoter causes expression of the detectable reporter.Certain other reporter assays are conducted with cells that harbor aheterologous construct that includes a transcriptional control elementthat activates expression of a polynucleotide of the invention and areporter operably linked thereto. Here, too, an agent that binds to thetranscriptional control element to activate expression of the reporteror that triggers the formation of an agent that binds to thetranscriptional control element to activate reporter expression, can beidentified by the generation of signal associated with reporterexpression.

The level of expression or activity can be compared to a baseline value.As indicated above, the baseline value can be a value for a controlsample or a statistical value that is representative of expressionlevels for a control population (e.g., healthy individuals not having orat risk for mood disorders or psychotic disorders). Expression levelscan also be determined for cells that do not express a polynucleotide ofthe invention as a negative control. Such cells generally are otherwisesubstantially genetically the same as the test cells.

A variety of different types of cells can be utilized in the reporterassays. Cells that express an endogenous polypeptide or polynucleotideof the invention include, e.g., brain cells, including cells from thecerebellum, anterior cingulate cortex, dorsolateral prefrontal cortex,amygdala, hippocampus, or nucleus accumbens. Cells that do notendogenously express polynucleotides of the invention can beprokaryotic, but are preferably eukaryotic. The eukaryotic cells can beany of the cells typically utilized in generating cells that harborrecombinant nucleic acid constructs. Exemplary eukaryotic cells include,but are not limited to, yeast, and various higher eukaryotic cells suchas the COS, CHO and HeLa cell lines.

Various controls can be conducted to ensure that an observed activity isauthentic including running parallel reactions with cells that lack thereporter construct or by not contacting a cell harboring the reporterconstruct with test compound. Compounds can also be further validated asdescribed below.

3. Catalytic Activity

Catalytic activity of polypeptides of the invention can be determined bymeasuring the production of enzymatic products or by measuring theconsumption of substrates. Activity refers to either the rate ofcatalysis or the ability to the polypeptide to bind (K_(m)) thesubstrate or release the catalytic product (K_(d)).

Analysis of the activity of polypeptides of the invention are performedaccording to general biochemical analyses. Such assays includecell-based assays as well as in vitro assays involving purified orpartially purified polypeptides or crude cell lysates. The assaysgenerally involve providing a known quantity of substrate andquantifying product as a function of time.

4. Validation

Agents that are initially identified by any of the foregoing screeningmethods can be further tested to validate the apparent activity.Preferably such studies are conducted with suitable animal models. Thebasic format of such methods involves administering a lead compoundidentified during an initial screen to an animal that serves as a modelfor humans and then determining if expression or activity of apolynucleotide or polypeptide of the invention is in fact upregulated.The animal models utilized in validation studies generally are mammalsof any kind. Specific examples of suitable animals include, but are notlimited to, primates, mice, and rats. As described herein, models usingadmininstration of known therapeutics can be useful.

5. Animal Models

Animal models of mental disorders also find use in screening formodulators. In one embodiment, invertebrate models such as Drosophilamodels can be used, screening for modulators of Drosophila orthologs ofthe human genes disclosed herein. In another embodiment, transgenicanimal technology including gene knockout technology, for example as aresult of homologous recombination with an appropriate gene targetingvector, or gene overexpression, will result in the absence, decreased orincreased expression of a polynucleotide or polypeptide of theinvention. The same technology can also be applied to make knockoutcells. When desired, tissue-specific expression or knockout of apolynucleotide or polypeptide of the invention may be necessary.Transgenic animals generated by such methods find use as animal modelsof mental illness and are useful in screening for modulators of mentalillness.

Knockout cells and transgenic mice can be made by insertion of a markergene or other heterologous gene into an endogenous gene site in themouse genome via homologous recombination. Such mice can also be made bysubstituting an endogenous polynucleotide of the invention with amutated version of the polynucleotide, or by mutating an endogenouspolynucleotide, e.g., by exposure to carcinogens.

For development of appropriate stem cells, a DNA construct is introducedinto the nuclei of embryonic stem cells. Cells containing the newlyengineered genetic lesion are injected into a host mouse embryo, whichis re-implanted into a recipient female. Some of these embryos developinto chimeric mice that possess germ cells partially derived from themutant cell line. Therefore, by breeding the chimeric mice it ispossible to obtain a new line of mice containing the introduced geneticlesion (see, e.g., Capecchi et al., Science 244:1288 (1989)). Chimerictargeted mice can be derived according to Hogan et al., Manipulating theMouse Embryo: A Laboratory Manual, Cold Spring Harbor Laboratory (1988)and Teratocarcinomas and Embryonic Stem Cells: A Practical Approach,Robertson, ed., IRL Press, Washington, D.C., (1987).

B. Modulators of Polypeptides or Polynucleotides of the Invention

The agents tested as modulators of the polypeptides or polynucleotidesof the invention can be any small chemical compound, or a biologicalentity, such as a protein, sugar, nucleic acid or lipid. Alternatively,modulators can be genetically altered versions of a polypeptide orpolynucleotide of the invention. Typically, test compounds will be smallchemical molecules and peptides. Essentially any chemical compound canbe used as a potential modulator or ligand in the assays of theinvention, although most often compounds that can be dissolved inaqueous or organic (especially DMSO-based) solutions are used. Theassays are designed to screen large chemical libraries by automating theassay steps and providing compounds from any convenient source toassays, which are typically run in parallel (e.g., in microtiter formatson microtiter plates in robotic assays). It will be appreciated thatthere are many suppliers of chemical compounds, including Sigma (St.Louis, Mo.), Aldrich (St. Louis, Mo.), Sigma-Aldrich (St. Louis, Mo.),Fluka Chemika-Biochemica Analytika (Buchs, Switzerland) and the like.Modulators also include agents designed to reduce the level of mRNA ofthe invention (e.g. antisense molecules, ribozymes, DNAzymes and thelike) or the level of translation from an mRNA.

In one preferred embodiment, high throughput screening methods involveproviding a combinatorial chemical or peptide library containing a largenumber of potential therapeutic compounds (potential modulator or ligandcompounds). Such “combinatorial chemical libraries” or “ligandlibraries” are then screened in one or more assays, as described herein,to identify those library members (particular chemical species orsubclasses) that display a desired characteristic activity. Thecompounds thus identified can serve as conventional “lead compounds” orcan themselves be used as potential or actual therapeutics.

A combinatorial chemical library is a collection of diverse chemicalcompounds generated by either chemical synthesis or biologicalsynthesis, by combining a number of chemical “building blocks” such asreagents. For example, a linear combinatorial chemical library such as apolypeptide library is formed by combining a set of chemical buildingblocks (amino acids) in every possible way for a given compound length(i.e., the number of amino acids in a polypeptide compound). Millions ofchemical compounds can be synthesized through such combinatorial mixingof chemical building blocks.

Preparation and screening of combinatorial chemical libraries is wellknown to those of skill in the art. Such combinatorial chemicallibraries include, but are not limited to, peptide libraries (see, e.g.,U.S. Pat. No. 5,010,175, Furka, Int. J. Pept. Prot. Res. 37:487-493(1991) and Houghton et al., Nature 354:84-88 (1991)). Other chemistriesfor generating chemical diversity libraries can also be used. Suchchemistries include, but are not limited to: peptoids (e.g., PCTPublication No. WO 91/19735), encoded peptides (e.g., PCT Publication WO93/20242), random bio-oligomers (e.g., PCT Publication No. WO 92/00091),benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomers such ashydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat.Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagiharaet al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidalpeptidomimetics with glucose scaffolding (Hirschmann et al., J. Amer.Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of smallcompound libraries (Chen et al., J. Amer. Chem. Soc. 116:2661 (1994)),oligocarbamates (Cho et al., Science 261:1303 (1993)), and/or peptidylphosphonates (Campbell et al., J. Org. Chem. 59:658 (1994)), nucleicacid libraries (see Ausubel, Berger and Sambrook, all supra), peptidenucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), antibodylibraries (see, e.g., Vaughn et al., Nature Biotechnology, 14(3):309-314(1996) and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang etal., Science, 274:1520-1522 (1996) and U.S. Pat. No. 5,593,853), smallorganic molecule libraries (see, e.g., benzodiazepines, Baum C&EN,January 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588;thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974;pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholinocompounds, U.S. Pat. No. 5,506,337; benzodiazepines, U.S. Pat. No.5,288,514, and the like).

Devices for the preparation of combinatorial libraries are commerciallyavailable (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, LouisvilleKy.; Symphony, Rainin, Woburn, Mass.; 433A Applied Biosystems, FosterCity, Calif.; 9050 Plus, Millipore, Bedford, Mass.). In addition,numerous combinatorial libraries are themselves commercially available(see, e.g., ComGenex, Princeton, N.J.; Tripos, Inc., St. Louis, Mo.; 3DPharmaceuticals, Exton, Pa.; Martek Biosciences, Columbia, Md., etc.).

C. Solid State and Soluble High Throughput Assays

In the high throughput assays of the invention, it is possible to screenup to several thousand different modulators or ligands in a single day.In particular, each well of a microtiter plate can be used to run aseparate assay against a selected potential modulator, or, ifconcentration or incubation time effects are to be observed, every 5-10wells can test a single modulator. Thus, a single standard microtiterplate can assay about 100 (e.g., 96) modulators. If 1536 well plates areused, then a single plate can easily assay from about 100 to about 1500different compounds. It is possible to assay several different platesper day; assay screens for up to about 6,000-20,000 different compoundsare possible using the integrated systems of the invention. Morerecently, microfluidic approaches to reagent manipulation have beendeveloped.

The molecule of interest can be bound to the solid state component,directly or indirectly, via covalent or non-covalent linkage, e.g., viaa tag. The tag can be any of a variety of components. In general, amolecule that binds the tag (a tag binder) is fixed to a solid support,and the tagged molecule of interest is attached to the solid support byinteraction of the tag and the tag binder.

A number of tags and tag binders can be used, based upon known molecularinteractions well described in the literature. For example, where a taghas a natural binder, for example, biotin, protein A, or protein G, itcan be used in conjunction with appropriate tag binders (avidin,streptavidin, neutravidin, the Fc region of an immunoglobulin, etc.).Antibodies to molecules with natural binders such as biotin are alsowidely available and appropriate tag binders (see, SIGMA Immunochemicals1998 catalogue SIGMA, St. Louis Mo.).

Similarly, any haptenic or antigenic compound can be used in combinationwith an appropriate antibody to form a tag/tag binder pair. Thousands ofspecific antibodies are commercially available and many additionalantibodies are described in the literature. For example, in one commonconfiguration, the tag is a first antibody and the tag binder is asecond antibody which recognizes the first antibody. In addition toantibody-antigen interactions, receptor-ligand interactions are alsoappropriate as tag and tag-binder pairs, such as agonists andantagonists of cell membrane receptors (e.g., cell receptor-ligandinteractions such as transferrin, c-kit, viral receptor ligands,cytokine receptors, chemokine receptors, interleukin receptors,immunoglobulin receptors and antibodies, the cadherin family, theintegrin family, the selectin family, and the like; see, e.g., Pigott &Power, The Adhesion Molecule Facts Book I (1993)). Similarly, toxins andvenoms, viral epitopes, hormones (e.g., opiates, steroids, etc.),intracellular receptors (e.g., which mediate the effects of varioussmall ligands, including steroids, thyroid hormone, retinoids andvitamin D; peptides), drugs, lectins, sugars, nucleic acids (both linearand cyclic polymer configurations), oligosaccharides, proteins,phospholipids and antibodies can all interact with various cellreceptors.

Synthetic polymers, such as polyurethanes, polyesters, polycarbonates,polyureas, polyamides, polyethyleneimines, polyarylene sulfides,polysiloxanes, polyimides, and polyacetates can also form an appropriatetag or tag binder. Many other tag/tag binder pairs are also useful inassay systems described herein, as would be apparent to one of skillupon review of this disclosure.

Common linkers such as peptides, polyethers, and the like can also serveas tags, and include polypeptide sequences, such as poly-Gly sequencesof between about 5 and 200 amino acids. Such flexible linkers are knownto those of skill in the art. For example, poly(ethelyne glycol) linkersare available from Shearwater Polymers, Inc., Huntsville, Ala. Theselinkers optionally have amide linkages, sulfhydryl linkages, orheterofunctional linkages.

Tag binders are fixed to solid substrates using any of a variety ofmethods currently available. Solid substrates are commonly derivatizedor functionalized by exposing all or a portion of the substrate to achemical reagent which fixes a chemical group to the surface which isreactive with a portion of the tag binder. For example, groups which aresuitable for attachment to a longer chain portion would include amines,hydroxyl, thiol, and carboxyl groups. Aminoalkylsilanes andhydroxyalkylsilanes can be used to functionalize a variety of surfaces,such as glass surfaces. The construction of such solid phase biopolymerarrays is well described in the literature (see, e.g., Merrifield, J.Am. Chem. Soc. 85:2149-2154 (1963) (describing solid phase synthesis of,e.g., peptides); Geysen et al., J. Immun. Meth. 102:259-274 (1987)(describing synthesis of solid phase components on pins); Frank andDoring, Tetrahedron 44:60316040 (1988) (describing synthesis of variouspeptide sequences on cellulose disks); Fodor et al., Science,251:767-777 (1991); Sheldon et al., Clinical Chemistry 39(4):718-719(1993); and Kozal et al., Nature Medicine 2(7):753759 (1996) (alldescribing arrays of biopolymers fixed to solid substrates).Non-chemical approaches for fixing tag binders to substrates includeother common methods, such as heat, cross-linking by UV radiation, andthe like.

The invention provides in vitro assays for identifying, in a highthroughput format, compounds that can modulate the expression oractivity of the polynucleotides or polypeptides of the invention. In apreferred embodiment, the methods of the invention include such acontrol reaction. For each of the assay formats described, “nomodulator” control reactions that do not include a modulator provide abackground level of binding activity.

In some assays it will be desirable to have positive controls to ensurethat the components of the assays are working properly. At least twotypes of positive controls are appropriate. First, a known activator ofa polynucleotide or polypeptide of the invention can be incubated withone sample of the assay, and the resulting increase in signal resultingfrom an increased expression level or activity of polynucleotide orpolypeptide determined according to the methods herein. Second, a knowninhibitor of a polynucleotide or polypeptide of the invention can beadded, and the resulting decrease in signal for the expression oractivity can be similarly detected.

D. Computer-Based Assays

Yet another assay for compounds that modulate the activity of apolypeptide or polynucleotide of the invention involves computerassisted drug design, in which a computer system is used to generate athree-dimensional structure of the polypeptide or polynucleotide basedon the structural information encoded by its amino acid or nucleotidesequence. The input sequence interacts directly and actively with apre-established algorithm in a computer program to yield secondary,tertiary, and quaternary structural models of the molecule. Similaranalyses can be performed on potential receptors or binding partners ofthe polypeptides or polynucleotides of the invention. The models of theprotein or nucleotide structure are then examined to identify regions ofthe structure that have the ability to bind, e.g., a polypeptide orpolynucleotide of the invention. These regions are then used to identifypolypeptides that bind to a polypeptide or polynucleotide of theinvention.

The three-dimensional structural model of a protein is generated byentering protein amino acid sequences of at least 10 amino acid residuesor corresponding nucleic acid sequences encoding a potential receptorinto the computer system. The amino acid sequences encoded by thenucleic acid sequences provided herein represent the primary sequencesor subsequences of the proteins, which encode the structural informationof the proteins. At least 10 residues of an amino acid sequence (or anucleotide sequence encoding 10 amino acids) are entered into thecomputer system from computer keyboards, computer readable substratesthat include, but are not limited to, electronic storage media (e.g.,magnetic diskettes, tapes, cartridges, and chips), optical media (e.g.,CD ROM), information distributed by internet sites, and by RAM. Thethree-dimensional structural model of the protein is then generated bythe interaction of the amino acid sequence and the computer system,using software known to those of skill in the art.

The amino acid sequence represents a primary structure that encodes theinformation necessary to form the secondary, tertiary, and quaternarystructure of the protein of interest. The software looks at certainparameters encoded by the primary sequence to generate the structuralmodel. These parameters are referred to as “energy terms,” and primarilyinclude electrostatic potentials, hydrophobic potentials, solventaccessible surfaces, and hydrogen bonding. Secondary energy termsinclude van der Waals potentials. Biological molecules form thestructures that minimize the energy terms in a cumulative fashion. Thecomputer program is therefore using these terms encoded by the primarystructure or amino acid sequence to create the secondary structuralmodel.

The tertiary structure of the protein encoded by the secondary structureis then formed on the basis of the energy terms of the secondarystructure. The user at this point can enter additional variables such aswhether the protein is membrane bound or soluble, its location in thebody, and its cellular location, e.g., cytoplasmic, surface, or nuclear.These variables along with the energy terms of the secondary structureare used to form the model of the tertiary structure. In modeling thetertiary structure, the computer program matches hydrophobic faces ofsecondary structure with like, and hydrophilic faces of secondarystructure with like.

Once the structure has been generated, potential ligand binding regionsare identified by the computer system. Three-dimensional structures forpotential ligands are generated by entering amino acid or nucleotidesequences or chemical formulas of compounds, as described above. Thethree-dimensional structure of the potential ligand is then compared tothat of a polypeptide or polynucleotide of the invention to identifybinding sites of the polypeptide or polynucleotide of the invention.Binding affinity between the protein and ligands is determined usingenergy terms to determine which ligands have an enhanced probability ofbinding to the protein.

Computer systems are also used to screen for mutations, polymorphicvariants, alleles and interspecies homologs of genes encoding apolypeptide or polynucleotide of the invention. Such mutations can beassociated with disease states or genetic traits and can be used fordiagnosis. As described above, GeneChip™ and related technology can alsobe used to screen for mutations, polymorphic variants, alleles andinterspecies homologs. Once the variants are identified, diagnosticassays can be used to identify patients having such mutated genes.Identification of the mutated a polypeptide or polynucleotide of theinvention involves receiving input of a first amino acid sequence of apolypeptide of the invention (or of a first nucleic acid sequenceencoding a polypeptide of the invention), e.g., any amino acid sequencehaving at least 60%, optionally at least 70% or 85%, identity with theamino acid sequence of interest, or conservatively modified versionsthereof. The sequence is entered into the computer system as describedabove. The first nucleic acid or amino acid sequence is then compared toa second nucleic acid or amino acid sequence that has substantialidentity to the first sequence. The second sequence is entered into thecomputer system in the manner described above. Once the first and secondsequences are compared, nucleotide or amino acid differences between thesequences are identified. Such sequences can represent allelicdifferences in various polynucleotides of the invention, and mutationsassociated with disease states and genetic traits.

VII. Compositions, Kits and Integrated Systems

The invention provides compositions, kits and integrated systems forpracticing the assays described herein using polypeptides orpolynucleotides of the invention, antibodies specific for polypeptidesor polynucleotides of the invention, etc.

The invention provides assay compositions for use in solid phase assays;such compositions can include, for example, one or more polynucleotidesor polypeptides of the invention immobilized on a solid support, and alabeling reagent. In each case, the assay compositions can also includeadditional reagents that are desirable for hybridization. Modulators ofexpression or activity of polynucleotides or polypeptides of theinvention can also be included in the assay compositions.

The invention also provides kits for carrying out the therapeutic anddiagnostic assays of the invention. The kits typically include a probethat comprises an antibody that specifically binds to polypeptides orpolynucleotides of the invention, and a label for detecting the presenceof the probe. The kits may include several polynucleotide sequencesencoding polypeptides of the invention. Kits can include any of thecompositions noted above, and optionally further include additionalcomponents such as instructions to practice a high-throughput method ofassaying for an effect on expression of the genes encoding thepolypeptides of the invention, or on activity of the polypeptides of theinvention, one or more containers or compartments (e.g., to hold theprobe, labels, or the like), a control modulator of the expression oractivity of polypeptides of the invention, a robotic armature for mixingkit components or the like.

The invention also provides integrated systems for high-throughputscreening of potential modulators for an effect on the expression oractivity of the polypeptides of the invention. The systems typicallyinclude a robotic armature which transfers fluid from a source to adestination, a controller which controls the robotic armature, a labeldetector, a data storage unit which records label detection, and anassay component such as a microtiter dish comprising a well having areaction mixture or a substrate comprising a fixed nucleic acid orimmobilization moiety.

A number of robotic fluid transfer systems are available, or can easilybe made from existing components. For example, a Zymate XP (ZymarkCorporation; Hopkinton, Mass.) automated robot using a Microlab 2200(Hamilton; Reno, Nev.) pipetting station can be used to transferparallel samples to 96 well microtiter plates to set up several parallelsimultaneous STAT binding assays.

Optical images viewed (and, optionally, recorded) by a camera or otherrecording device (e.g., a photodiode and data storage device) areoptionally further processed in any of the embodiments herein, e.g., bydigitizing the image and storing and analyzing the image on a computer.A variety of commercially available peripheral equipment and software isavailable for digitizing, storing and analyzing a digitized video ordigitized optical image, e.g., using PC (Intel ×86 or Pentiumchip-compatible DOS®, OS2® WINDOWS®, WINDOWS NT®, WINDOWS95®,WINDOWS98®, or WINDOWS2000® based computers), MACINTOSH®, or UNIX® based(e.g., SUN® work station) computers.

One conventional system carries light from the specimen field to acooled charge-coupled device (CCD) camera, in common use in the art. ACCD camera includes an array of picture elements (pixels). The lightfrom the specimen is imaged on the CCD. Particular pixels correspondingto regions of the specimen (e.g., individual hybridization sites on anarray of biological polymers) are sampled to obtain light intensityreadings for each position. Multiple pixels are processed in parallel toincrease speed. The apparatus and methods of the invention are easilyused for viewing any sample, e.g., by fluorescent or dark fieldmicroscopic techniques.

VIII. Administration and Pharmaceutical Compositions

Modulators of the polynucleotides or polypeptides of the invention(e.g., antagonists or agonists) can be administered directly to amammalian subject for modulation of activity of those molecules in vivo.Administration is by any of the routes normally used for introducing amodulator compound into ultimate contact with the tissue to be treatedand is well known to those of skill in the art. Although more than oneroute can be used to administer a particular composition, a particularroute can often provide a more immediate and more effective reactionthan another route.

Diseases that can be treated include the following, which include thecorresponding reference number from Morrison, DSM-IV Made Easy, 1995:Schizophrenia, Catatonic, Subchronic, (295.21); Schizophrenia,Catatonic, Chronic (295.22); Schizophrenia, Catatonic, Subchronic withAcute Exacerbation (295.23); Schizophrenia, Catatonic, Chronic withAcute Exacerbation (295.24); Schizophrenia, Catatonic, in Remission(295.55); Schizophrenia, Catatonic, Unspecified (295.20); Schizophrenia,Disorganized, Subchronic (295.11); Schizophrenia, Disorganized, Chronic(295.12); Schizophrenia, Disorganized, Subchronic with AcuteExacerbation (295.13); Schizophrenia, Disorganized, Chronic with AcuteExacerbation (295.14); Schizophrenia, Disorganized, in Remission(295.15); Schizophrenia, Disorganized, Unspecified (295.10);Schizophrenia, Paranoid, Subchronic (295.31); Schizophrenia, Paranoid,Chronic (295.32); Schizophrenia, Paranoid, Subchronic with AcuteExacerbation (295.33); Schizophrenia, Paranoid, Chronic with AcuteExacerbation (295.34); Schizophrenia, Paranoid, in Remission (295.35);Schizophrenia, Paranoid, Unspecified (295.30); Schizophrenia,Undifferentiated, Subchronic (295.91); Schizophrenia, Undifferentiated,Chronic (295.92); Schizophrenia, Undifferentiated, Subchronic with AcuteExacerbation (295.93); Schizophrenia, Undifferentiated, Chronic withAcute Exacerbation (295.94); Schizophrenia, Undifferentiated, inRemission (295.95); Schizophrenia, Undifferentiated, Unspecified(295.90); Schizophrenia, Residual, Subchronic (295.61); Schizophrenia,Residual, Chronic (295.62); Schizophrenia, Residual, Subchronic withAcute Exacerbation (295.63); Schizophrenia, Residual, Chronic with AcuteExacerbation (295.94); Schizophrenia, Residual, in Remission (295.65);Schizophrenia, Residual, Unspecified (295.60); Delusional (Paranoid)Disorder (297.10); Brief Reactive Psychosis (298.80); SchizophreniformDisorder (295.40); Schizoaffective Disorder (295.70); Induced PsychoticDisorder (297.30); Psychotic Disorder NOS (Atypical Psychosis) (298.90);Personality Disorders, Paranoid (301.00); Personality Disorders,Schizoid (301.20); Personality Disorders, Schizotypal (301.22);Personality Disorders, Antisocial (301.70); Personality Disorders,Borderline (301.83) and bipolar disorders, maniac, hypomaniac, dysthymicor cyclothymic disorders, substance-induced mood disorders, majordepression, psychosis, including paranoid psychosis, catatonicpsychosis, delusional psychosis, having schizoaffective disorder, andsubstance-induced psychotic disorder.

In some embodiments, modulators of polynucleotides or polypeptides ofthe invention can be combined with other drugs useful for treatingmental disorders including useful for treating mood disorders, e.g.,schizophrenia, bipolar disorders, or major depression. In some preferredembodiments, pharmaceutical compositions of the invention comprise amodulator of a polypeptide of polynucleotide of the invention combinedwith at least one of the compounds useful for treating schizophrenia,bipolar disorder, or major depression, e.g., such as those described inU.S. Pat. Nos. 6,297,262; 6,284,760; 6,284,771; 6,232,326; 6,187,752;6,117,890; 6,239,162 or 6,166,008.

The pharmaceutical compositions of the invention may comprise apharmaceutically acceptable carrier. Pharmaceutically acceptablecarriers are determined in part by the particular composition beingadministered, as well as by the particular method used to administer thecomposition. Accordingly, there is a wide variety of suitableformulations of pharmaceutical compositions of the present invention(see, e.g., Remington's Pharmaceutical Sciences, 17^(th) ed. 1985)).

The modulators (e.g., agonists or antagonists) of the expression oractivity of the a polypeptide or polynucleotide of the invention, aloneor in combination with other suitable components, can be made intoaerosol formulations (i.e., they can be “nebulized”) to be administeredvia inhalation or in compositions useful for injection. Aerosolformulations can be placed into pressurized acceptable propellants, suchas dichlorodifluoromethane, propane, nitrogen, and the like.

Formulations suitable for administration include aqueous and non-aqueoussolutions, isotonic sterile solutions, which can contain antioxidants,buffers, bacteriostats, and solutes that render the formulationisotonic, and aqueous and non-aqueous sterile suspensions that caninclude suspending agents, solubilizers, thickening agents, stabilizers,and preservatives. In the practice of this invention, compositions canbe administered, for example, orally, nasally, topically, intravenously,intraperitoneally, or intrathecally. The formulations of compounds canbe presented in unit-dose or multi-dose sealed containers, such asampoules and vials. Solutions and suspensions can be prepared fromsterile powders, granules, and tablets of the kind previously described.The modulators can also be administered as part of a prepared food ordrug.

The dose administered to a patient, in the context of the presentinvention should be sufficient to effect a beneficial response in thesubject over time. The optimal dose level for any patient will depend ona variety of factors including the efficacy of the specific modulatoremployed, the age, body weight, physical activity, and diet of thepatient, on a possible combination with other drugs, and on the severityof the mental disorder. The size of the dose also will be determined bythe existence, nature, and extent of any adverse side effects thataccompany the administration of a particular compound or vector in aparticular subject.

In determining the effective amount of the modulator to be administereda physician may evaluate circulating plasma levels of the modulator,modulator toxicity, and the production of anti-modulator antibodies. Ingeneral, the dose equivalent of a modulator is from about 1 ng/kg to 10mg/kg for a typical subject.

For administration, modulators of the present invention can beadministered at a rate determined by the LD-50 of the modulator, and theside effects of the modulator at various concentrations, as applied tothe mass and overall health of the subject. Administration can beaccomplished via single or divided doses.

IX. Gene Therapy Applications

A variety of human diseases can be treated by therapeutic approachesthat involve stably introducing a gene into a human cell such that thegene is transcribed and the gene product is produced in the cell.Diseases amenable to treatment by this approach include inheriteddiseases, including those in which the defect is in a single or multiplegenes. Gene therapy is also useful for treatment of acquired diseasesand other conditions. For discussions on the application of gene therapytowards the treatment of genetic as well as acquired diseases, see,Miller, Nature 357:455-460 (1992); and Mulligan, Science 260:926-932(1993).

In the context of the present invention, gene therapy can be used fortreating a variety of disorders and/or diseases in which thepolynucleotides and polypeptides of the invention has been implicated.For example, compounds, including polynucleotides, can be identified bythe methods of the present invention as effective in treating a mentaldisorder. Introduction by gene therapy of these polynucleotides can thenbe used to treat, e.g., mental disorders including mood disorders andpsychotic disorders.

A. Vectors for Gene Delivery

For delivery to a cell or organism, the polynucleotides of the inventioncan be incorporated into a vector. Examples of vectors used for suchpurposes include expression plasmids capable of directing the expressionof the nucleic acids in the target cell. In other instances, the vectoris a viral vector system wherein the nucleic acids are incorporated intoa viral genome that is capable of transfecting the target cell. In apreferred embodiment, the polynucleotides can be operably linked toexpression and control sequences that can direct expression of the genein the desired target host cells. Thus, one can achieve expression ofthe nucleic acid under appropriate conditions in the target cell.

B. Gene Delivery Systems

Viral vector systems useful in the expression of the nucleic acidsinclude, for example, naturally occurring or recombinant viral vectorsystems. Depending upon the particular application, suitable viralvectors include replication competent, replication deficient, andconditionally replicating viral vectors. For example, viral vectors canbe derived from the genome of human or bovine adenoviruses, vacciniavirus, herpes virus, adeno-associated virus, minute virus of mice (MVM),HIV, sindbis virus, and retroviruses (including but not limited to Roussarcoma virus), and MoMLV. Typically, the genes of interest are insertedinto such vectors to allow packaging of the gene construct, typicallywith accompanying viral DNA, followed by infection of a sensitive hostcell and expression of the gene of interest.

As used herein, “gene delivery system” refers to any means for thedelivery of a nucleic acid of the invention to a target cell. In someembodiments of the invention, nucleic acids are conjugated to a cellreceptor ligand for facilitated uptake (e.g., invagination of coatedpits and internalization of the endosome) through an appropriate linkingmoiety, such as a DNA linking moiety (Wu et al., J. Biol. Chem.263:14621-14624 (1988); WO 92/06180). For example, nucleic acids can belinked through a polylysine moiety to asialo-oromucocid, which is aligand for the asialoglycoprotein receptor of hepatocytes.

Similarly, viral envelopes used for packaging gene constructs thatinclude the nucleic acids of the invention can be modified by theaddition of receptor ligands or antibodies specific for a receptor topermit receptor-mediated endocytosis into specific cells (see, e.g., WO93/20221, WO 93/14188, and WO 94/06923). In some embodiments of theinvention, the DNA constructs of the invention are linked to viralproteins, such as adenovirus particles, to facilitate endocytosis(Curiel et al., Proc. Natl. Acad. Sci. U.S.A. 88:8850-8854 (1991)). Inother embodiments, molecular conjugates of the instant invention caninclude microtubule inhibitors (WO/9406922), synthetic peptidesmimicking influenza virus hemagglutinin (Plank et al., J. Biol. Chem.269:12918-12924 (1994)), and nuclear localization signals such as SV40 Tantigen (WO93/19768).

Retroviral vectors are also useful for introducing the nucleic acids ofthe invention into target cells or organisms. Retroviral vectors areproduced by genetically manipulating retroviruses. The viral genome ofretroviruses is RNA. Upon infection, this genomic RNA is reversetranscribed into a DNA copy which is integrated into the chromosomal DNAof transduced cells with a high degree of stability and efficiency. Theintegrated DNA copy is referred to as a provirus and is inherited bydaughter cells as is any other gene. The wild type retroviral genome andthe proviral DNA have three genes: the gag, the pol and the env genes,which are flanked by two long terminal repeat (LTR) sequences. The gaggene encodes the internal structural (nucleocapsid) proteins; the polgene encodes the RNA directed DNA polymerase (reverse transcriptase);and the env gene encodes viral envelope glycoproteins. The 5′ and 3′LTRs serve to promote transcription and polyadenylation of virion RNAs.Adjacent to the 5′ LTR are sequences necessary for reverse transcriptionof the genome (the tRNA primer binding site) and for efficientencapsulation of viral RNA into particles (the Psi site) (see, Mulligan,In: Experimental Manipulation of Gene Expression, Inouye (ed), 155-173(1983); Mann et al., Cell 33:153-159 (1983); Cone and Mulligan,Proceedings of the National Academy of Sciences, U.S.A., 81:6349-6353(1984)).

The design of retroviral vectors is well known to those of ordinaryskill in the art. In brief, if the sequences necessary for encapsidation(or packaging of retroviral RNA into infectious virions) are missingfrom the viral genome, the result is a cis-acting defect which preventsencapsidation of genomic RNA. However, the resulting mutant is stillcapable of directing the synthesis of all virion proteins. Retroviralgenomes from which these sequences have been deleted, as well as celllines containing the mutant genome stably integrated into the chromosomeare well known in the art and are used to construct retroviral vectors.Preparation of retroviral vectors and their uses are described in manypublications including, e.g., European Patent Application EPA 0 178 220;U.S. Pat. No. 4,405,712, Gilboa Biotechniques 4:504-512 (1986); Mann etal., Cell 33:153-159 (1983); Cone and Mulligan Proc. Natl. Acad. Sci.USA 81:6349-6353 (1984); Eglitis et al. Biotechniques 6:608-614 (1988);Miller et al. Biotechniques 7:981-990 (1989); Miller (1992) supra;Mulligan (1993), supra; and WO 92/07943.

The retroviral vector particles are prepared by recombinantly insertingthe desired nucleotide sequence into a retrovirus vector and packagingthe vector with retroviral capsid proteins by use of a packaging cellline. The resultant retroviral vector particle is incapable ofreplication in the host cell but is capable of integrating into the hostcell genome as a proviral sequence containing the desired nucleotidesequence. As a result, the patient is capable of producing, for example,a polypeptide or polynucleotide of the invention and thus restore thecells to a normal phenotype.

Packaging cell lines that are used to prepare the retroviral vectorparticles are typically recombinant mammalian tissue culture cell linesthat produce the necessary viral structural proteins required forpackaging, but which are incapable of producing infectious virions. Thedefective retroviral vectors that are used, on the other hand, lackthese structural genes but encode the remaining proteins necessary forpackaging. To prepare a packaging cell line, one can construct aninfectious clone of a desired retrovirus in which the packaging site hasbeen deleted. Cells comprising this construct will express allstructural viral proteins, but the introduced DNA will be incapable ofbeing packaged. Alternatively, packaging cell lines can be produced bytransforming a cell line with one or more expression plasmids encodingthe appropriate core and envelope proteins. In these cells, the gag,pol, and env genes can be derived from the same or differentretroviruses.

A number of packaging cell lines suitable for the present invention arealso available in the prior art. Examples of these cell lines includeCrip, GPE86, PA317 and PG13 (see Miller et al., J. Virol. 65:2220-2224(1991)). Examples of other packaging cell lines are described in Coneand Mulligan Proceedings of the National Academy of Sciences, USA,81:6349-6353 (1984); Danos and Mulligan Proceedings of the NationalAcademy of Sciences, USA, 85:6460-6464 (1988); Eglitis et al. (1988),supra; and Miller (1990), supra.

Packaging cell lines capable of producing retroviral vector particleswith chimeric envelope proteins may be used. Alternatively, amphotropicor xenotropic envelope proteins, such as those produced by PA317 and GPXpackaging cell lines may be used to package the retroviral vectors.

In some embodiments of the invention, an antisense polynucleotide isadministered which hybridizes to a gene encoding a polypeptide of theinvention. The antisense polypeptide can be provided as an antisenseoligonucleotide (see, e.g., Murayama et al., Antisense Nucleic Acid DrugDev. 7:109-114 (1997)). Genes encoding an antisense nucleic acid canalso be provided; such genes can be introduced into cells by methodsknown to those of skill in the art. For example, one can introduce anantisense nucleotide sequence in a viral vector, such as, for example,in hepatitis B virus (see, e.g., Ji et al., J. Viral Hepat. 4:167-173(1997)), in adeno-associated virus (see, e.g., Xiao et al., Brain Res.756:76-83 (1997)), or in other systems including, but not limited, to anHVJ (Sendai virus)-liposome gene delivery system (see, e.g., Kaneda etal., Ann. NY Acad. Sci. 811:299-308 (1997)), a “peptide vector” (see,e.g., Vidal et al., CR Acad. Sci III 32:279-287 (1997)), as a gene in anepisomal or plasmid vector (see, e.g., Cooper et al., Proc. Natl. Acad.Sci. U.S.A. 94:6450-6455 (1997), Yew et al. Hum Gene Ther. 8:575-584(1997)), as a gene in a peptide-DNA aggregate (see, e.g., Niidome etal., J. Biol. Chem. 272:15307-15312 (1997)), as “naked DNA” (see, e.g.,U.S. Pat. Nos. 5,580,859 and 5,589,466), in lipidic vector systems (see,e.g., Lee et al., Crit Rev Ther Drug Carrier Syst. 14:173-206 (1997)),polymer coated liposomes (U.S. Pat. Nos. 5,213,804 and 5,013,556),cationic liposomes (Epand et al., U.S. Pat. Nos. 5,283,185; 5,578,475;5,279,833; and 5,334,761), gas filled microspheres (U.S. Pat. No.5,542,935), ligand-targeted encapsulated macromolecules (U.S. Pat. Nos.5,108,921; 5,521,291; 5,554,386; and 5,166,320).

Upregulated transcripts listed in the biomarker tables herein which arecorrelated with mental disorders may be targeted with one or more shortinterfering RNA (siRNA) sequences that hybridize to specific sequencesin the target, as described above. Targeting of certain braintranscripts with siRNA in vivo has been reported, for example, by Zhanget al., J. Gene. Med., 12:1039-45 (2003), who utilized monoclonalantibodies against the transferrin receptor to facilitate passage ofliposome-encapsulated siRNA molecules through the blood brain barrier.Targeted siRNAs represent useful therapeutic compounds for attenuatingthe over-expressed transcripts that are associated with disease states,e.g., MDD, BP, and other mental disorders.

In another embodiment, conditional expression systems, such as thosetypified by the tet-regulated systems and the RU-486 system, can be used(see, e.g., Gossen & Bujard, PNAS 89:5547 (1992); Oligino et al., GeneTher. 5:491-496 (1998); Wang et al., Gene Ther. 4:432-441 (1997);Neering et al., Blood 88:1147-1155 (1996); and Rendahl et al., Nat.Biotechnol. 16:757-761 (1998)). These systems impart small moleculecontrol on the expression of the target gene(s) of interest.

In another embodiment, stem cells engineered to express a transcript ofinterest can implanted into the brain.

C. Pharmaceutical Formulations

When used for pharmaceutical purposes, the vectors used for gene therapyare formulated in a suitable buffer, which can be any pharmaceuticallyacceptable buffer, such as phosphate buffered saline or sodiumphosphate/sodium sulfate, Tris buffer, glycine buffer, sterile water,and other buffers known to the ordinarily skilled artisan such as thosedescribed by Good et al. Biochemistry 5:467 (1966).

The compositions can additionally include a stabilizer, enhancer, orother pharmaceutically acceptable carriers or vehicles. Apharmaceutically acceptable carrier can contain a physiologicallyacceptable compound that acts, for example, to stabilize the nucleicacids of the invention and any associated vector. A physiologicallyacceptable compound can include, for example, carbohydrates, such asglucose, sucrose or dextrans; antioxidants, such as ascorbic acid orglutathione; chelating agents; low molecular weight proteins or otherstabilizers or excipients. Other physiologically acceptable compoundsinclude wetting agents, emulsifying agents, dispersing agents, orpreservatives, which are particularly useful for preventing the growthor action of microorganisms. Various preservatives are well known andinclude, for example, phenol and ascorbic acid. Examples of carriers,stabilizers, or adjuvants can be found in Remington's PharmaceuticalSciences, Mack Publishing Company, Philadelphia, Pa., 17th ed. (1985).

D. Administration of Formulations

The formulations of the invention can be delivered to any tissue ororgan using any delivery method known to the ordinarily skilled artisan.In some embodiments of the invention, the nucleic acids of the inventionare formulated in mucosal, topical, and/or buccal formulations,particularly mucoadhesive gel and topical gel formulations. Exemplarypermeation enhancing compositions, polymer matrices, and mucoadhesivegel preparations for transdermal delivery are disclosed in U.S. Pat. No.5,346,701.

E. Methods of Treatment

The gene therapy formulations of the invention are typicallyadministered to a cell. The cell can be provided as part of a tissue,such as an epithelial membrane, or as an isolated cell, such as intissue culture. The cell can be provided in vivo, ex vivo, or in vitro.

The formulations can be introduced into the tissue of interest in vivoor ex vivo by a variety of methods. In some embodiments of theinvention, the nucleic acids of the invention are introduced into cellsby such methods as microinjection, calcium phosphate precipitation,liposome fusion, or biolistics. In further embodiments, the nucleicacids are taken up directly by the tissue of interest.

In some embodiments of the invention, the nucleic acids of the inventionare administered ex vivo to cells or tissues explanted from a patient,then returned to the patient. Examples of ex vivo administration oftherapeutic gene constructs include Nolta et al., Proc Natl. Acad. Sci.USA 93(6):2414-9 (1996); Koc et al., Seminars in Oncology 23 (1):46-65(1996); Raper et al., Annals of Surgery 223(2):116-26 (1996); Dalesandroet al., J. Thorac. Cardi. Surg., 11(2):416-22 (1996); and Makarov etal., Proc. Natl. Acad. Sci. USA 93(1):402-6 (1996).

X. Diagnosis of Mood Disorders and Psychotic Disorders

The present invention also provides methods of diagnosing mood disorders(such as major depression or bipolar disorder), psychotic disorders(such as schizophrenia), or a predisposition of at least some of thepathologies of such disorders. Diagnosis involves determining the levelof a polypeptide or polynucleotide of the invention in a patient andthen comparing the level to a baseline or range. Typically, the baselinevalue is representative of a polypeptide or polynucleotide of theinvention in a healthy person not suffering from a mood disorder or apsychotic disorder or under the effects of medication or other drugs.Variation of levels of a polypeptide or polynucleotide of the inventionfrom the baseline range (either up or down) indicates that the patienthas a mood disorder or a psychotic disorder or at risk of developing atleast some aspects of a mood disorder or a psychotic disorder. In someembodiments, the level of a polypeptide or polynucleotide of theinvention are measured by taking a blood, urine or tissue sample from apatient and measuring the amount of a polypeptide or polynucleotide ofthe invention in the sample using any number of detection methods, suchas those discussed herein.

Antibodies can be used in assays to detect differential proteinexpression in patient samples, e.g., ELISA assays, immunoprecipitationassays, and immunohistochemical assays. PCR assays can be used to detectexpression levels of nucleic acids, as well as to discriminate betweenvariants in genomic structure, such as insertion/deletion mutations(e.g., PSPHL).

In the case where absence of gene expression is associated with adisorder, the genomic structure of a gene such as PSPHL can be evaluatedwith known methods such as PCR to detect deletion or insertion mutationsassociated with disease suspectibility. Conversely, the presence of mRNAor protein corresponding to the PSPHL gene would indicate that anindividual does not have the PSPHL deletion associated withsusceptibility to BP. Thus, diagnosis can be made by detecting thepresence or absence of mRNA or protein, or by examining the genomicstructure of the gene. Any combination of exons or non-transcribedregions can be used to detect the deletion allele. For example, thepresence of exon 4 but not exons 1, 2, and/or 3 would indicate thepresence of the deletion allele. Similarly, deletion of the promoterregion would indicate the deletion allele. Any significant mRNAdetection, especially detection of an mRNA comprising exons 1, 2, and/or3, would indicate the absence of the deletion allele, which is nottranscribed due to the promoter deletion.

Single nucleotide polymorphism (SNP) analysis is also useful fordetecting differences between alleles of the polynucleotides (e.g.,genes) of the invention. SNPs linked to genes encoding polypeptides ofthe invention are useful, for instance, for diagnosis of diseases (e.g.,mood disorders such as bipolar disease, major depression, andschizophrenia disorders) whose occurrence is linked to the genesequences of the invention. For example, if an individual carries atleast one SNP linked to a disease-associated allele of the genesequences of the invention, the individual is likely predisposed for oneor more of those diseases. If the individual is homozygous for adisease-linked SNP, the individual is particularly predisposed foroccurrence of that disease. In some embodiments, the SNP associated withthe gene sequences of the invention is located within 300,000; 200,000;100,000; 75,000; 50,000; or 10,000 base pairs from the gene sequence.

Various real-time PCR methods can be used to detect SNPs, including,e.g., Taqman or molecular beacon-based assays (e.g., U.S. Pat. Nos.5,210,015; 5,487,972; Tyagi et al., Nature Biotechnology 14:303 (1996);and PCT WO 95/13399 are useful to monitor for the presence of absence ofa SNP. Additional SNP detection methods include, e.g., DNA sequencing,sequencing by hybridization, dot blotting, oligonucleotide array (DNAChip) hybridization analysis, or are described in, e.g., U.S. Pat. No.6,177,249; Landegren et al., Genome Research, 8:769-776 (1998); Botsteinet al., Am J Human Genetics 32:314-331 (1980); Meyers et al., Methods inEnzymology 155:501-527 (1987); Keen et al., Trends in Genetics 7:5(1991); Myers et al., Science 230:1242-1246 (1985); and Kwok et al.,Genomics 23:138-144 (1994). PCR methods can also be used to detectdeletion/insertion polymorphisms, such as the deletion polymorphism ofthe PSPHL gene associated with suspectibility to BP.

In some embodiments, the level of the enzymatic product of a polypeptideor polynucleotide of the invention is measured and compared to abaseline value of a healthy person or persons. Modulated levels of theproduct compared to the baseline indicates that the patient has a mooddisorder or a psychotic disorder or is at risk of developing at leastsome aspects of a mood disorder or a psychotic disorder. Patientsamples, for example, can be blood, urine or tissue samples.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims.

EXAMPLES Example 1 Identification of FGF Pathway Genes Dysregulated inMDD

Major depressive disorder (MDD) and bipolar disorder (BP) are affectivediseases that strike a significant proportion of the population. Thesecomplex genetic disorders arise from the interplay of vulnerabilitygenes and environmental stressors, impacting neural circuits thatcontrol mood. Beyond the role of limbic structures, mood disorders arehypothesized to involve aberrant activity of the cerebral cortex. Thus,imaging techniques have implicated the dorsolateral prefrontal (DLPFC)and anterior cingulate (AnCg) cortices in mood disorders since affectedsubjects display changes in volumetric measurements (Harrison, P. J.Brain 125, 1428-49 (2002).) and altered activity in response to acognitive challenge. (Kruger, S., Seminowicz, D., Goldapple, K.,Kennedy, S. H. & Mayberg, H. S. Biol Psychiatry 54, 1274-83 (2003))Using a candidate approach, studies have demonstrated altered corticalexpression of specific neurotransmitter- and stress-related genes inaffective illness. However, the full extent of the alteration incortical activity had not been described, nor had an unbiased“discovery” approach been applied to characterize it.

We have applied microarray technology to the study of DLPFC and AnCg inpost-mortem samples from MDD, BP and non-psychiatric controls. Thisrepresents the first transcriptional profiling study demonstratingsignificant alterations of gene expression in major depression, and thefirst one contrasting the two major mood disorders (MDD and BP) with thesame group of controls. Here we report the dysregulation of fibroblastgrowth factor (FGF) system transcripts specifically in MDD.

Human Studies

The studies were carried out in a carefully selected cohort ofpostmortem human brains, and replicated in a separate cohort (see Table1a and 1b). The Affymetrix HG-133A array contains probe sets for 21 FGFsystem transcripts, including all 4 receptors (FGFR1, 2, 3, 4) and 12FGF peptide ligands (FGF1, 2, 3, 5, 6, 7, 8, 9, 12, 13, 14, 17, 18, 20,21, 22, 23). Of these only 10 were reliably detected in the regionsassayed and include three of the FGF receptors (FGFR1, 2, and 3) andseven FGF ligands (FGF1, 2, 7, 9, 12, 13,14). Of the ten FGF transcriptsreliably detected, seven were significantly altered in one of the tworegions studied—four were significantly differentially expressed in theDLPFC of MDD subjects, including 2 FGF receptors (FGFR2 and 3) and 2 FGFligands (FGF1 and 9); and six were significantly differentiallyexpressed in the AnCg including two receptors (FGFR2 and 3) and fourligands (FGF1, 2, 9 and 12). The probability that this family ofmolecules would have emerged by chance, based on a hypergeometricdistribution, is p<0.001. These data are summarized in Table 2, whichalso reports on the transcripts confirmed by real-time PCR analysisand/or those replicated in a second independent cohort of MDD andcontrol subjects. Importantly, none of the above transcripts wereobserved to be differentially expressed in BP by microarray in eithercohort or by real-time PCR analysis, demonstrating the specificity ofthis dysregulation for MDD.

Given this selective dysregulation of FGF system transcripts in MDD weasked whether these changes might be secondary to antidepressant therapysince a subset of the subjects was on antidepressants, and the majorityof those were on specific serotonin reuptake inhibitors (SSRI's). Thus,we separated our microarray data into MDD subjects prescribed SSRI's(n=5) and those not prescribed SSRI's (n=4) for statistical comparisons.This analysis showed that FGFR3 and FGF2 had a tendency towardup-regulation (p=0.15 and 0.07, respectively) and that FGF 9 showed atendency toward down-regulation (p=0.12) by SSRI treatment, all opposingthe directionality of dysregulation we see in MDD subjects relative tocontrols. No other FGF system transcripts approached significantdifferences in this analysis. These data strongly suggest that ourobservations are not secondary to SSRI treatment. Furthermore, theobserved attenuation of FGF transcript dysregulation in the SSRIprescribed group suggests that the normalization of FGF system might beone mechanism of action of this class of drugs since several FGFtranscripts appear to be altered in severe depression and are partiallyreversed by SSRI therapy.

Rodent Anatomical Studies, Effect of Fluoxetine.

We studied the anatomical expression of FGFR2 in rats subjected tochronic fluoxetine treatment relative to controls (FIG. 1). FGFR2 mRNAexpression was quantified in the retrosplenial cortex and in thehippocampus since this area has recently been implicated in the mode ofaction of antidepressants (Santarelli, L. et al. Science 301, 805-9(2003)). Results show that FGFR2 message is significantly increased byfluoxetine in all hippocampal subfields (CA1, CA2, CA3, and dentategyrus) and the retrosplenial cortex (Fisher's PLSD, p=0.0049).

The implication of the FGF system in MDD has emerged from our studiesutilizing microarray technology to study human psychiatric illness.Other growth factors have been hypothesized to contribute to theetiology and maintenance of such illnesses and can offer a framework inwhich to place our own findings. Most notably, brain derivedneurotrophic factor (BDNF) has been repeatedly implicated in MDD, BP andin SZ. BDNF mRNA levels are reportedly decreased in the DLPFC (Weickert,C. S., et al., Mol Psychiatry 8, 592-610 (2003)) of schizophrenics andBDNF protein levels are decreased in serum of MDD (Shimizu, E. et al.Biol Psychiatry 54, 70-5 (2003)) patients. Furthermore, BDNF expressionis regulated by antipsychotic (Chlan-Fourney, J. et al., Brain Res 954,11-20 (2002)) and antidepressant drugs (Shimizu, E. et al. BiolPsychiatry 54, 70-5 (2003)), (Dias, B. G., et al., Neuropharmacology 45,553-63 (2003)). A smaller volume of literature implicates other growthfactors, including nerve growth factor (Parikh, V., Evans, D. R., Khan,M. M. & Mahadik, S. P. Schizophr Res 60, 117-23 (2003)), epidermalgrowth factor (Futamura, T. et al. Mol Psychiatry 7, 673-82 (2002)) andneurotrophin-3 (Hock, C. et al. Mol Psychiatry 5, 510-3 (2000)) inpsychiatric illness.

Growth factors play significant roles in development and maintenance ofthe central nervous system. In the developing brain, they are involvedin specific neuronal terminal differentiation and migration toappropriate subfields. In the adult brain they are critical in neuronalsurvival, axonal branching and synaptic plasticity. Specifically, FGF2(Viti, J., Gulacsi, A. & Lillien, L. J Neurosci 23, 5919-27 (2003)) andFGF8 (Gunhaga, L. et al. Nat Neurosci 6, 701-7 (2003)) have been shownto interact with Wnt in the development of the cortex in mouse and chickembryos, respectively. In the adult brain, FGF2 promotes neuronalsurvival and axonal branching (Abe, K. & Saito, H. Pharmacol Res 43,307-12 (2001)) and its expression is modulated by stress (Molteni, R. etal., Brain Res Rev 37, 249-58 (2001)).

Together, these results lead to the novel hypothesis that dysregulationof the FGF system contributes to either the vulnerability to MDD or theexpression of the illness, and that antidepressants might attenuate thisdysregulation. Animal models will be crucial for defining theinvolvement of the FGF system in emotionality and elucidating its rolein neural plasticity and antidepressant action.

Example 2 Identification of Novel Insertion/Deletion Polymorphism inPSPHL Gene and Association of Deletion Mutation with BP Susceptibility

Evaluation of PSPHL expression in anterior cingulated cortex byquantitative RT-PCR reveals that PSPHL shows a dichotomous (present orabsent) pattern of expression among individuals. In our first cohort,none of the 9 BPD patients (0%) shows PSPHL expression, while 7 out of11 MDD patients (64%) and 8 out of 20 controls (40%) show sufficientexpression of PSPHL. The probability of distribution of thepresent/absent expression pattern between BPD and controls is 0.018, andbetween MDD and controls is 0.105 based on the Fisher exact test. Toassure this significant contrast between BPD and controls, we measuredPSPHL expression in an additional 9 BPD and 20 control individuals (fora total of 18 BPD and 40 controls) using quantitative RT-PCR. In thislarger sample set, none of the 18 BPD patients (0%) shows any expressionof PSPHL, while 16 out of 40 controls (40%) show sufficient expressionof the transcript (p value=0.0008).

The fact that PSPHL shows dichotomous present/absent pattern ofexpression among individuals with brain-wide consistency suggestsgenetic variation in its regulation. Since genomic organization of PSPHLhas not been characterized (Planitzer, supra (1998)), we have identifiedgenomic organization of PSPHL as shown in FIG. 14. The PSPHL geneconsists of 4 exons. Exons 1, 2, 3 and 4 are 213 bp, 114 bp, 122 bp and501 bp, in length, respectively, and span introns 1, 2 and 3 (3221bp,829 bp and 11939 bp, in length, respectively). Further, the PSPHL genehas two alternative transcripts, one of which utilizes the exons 1-4(PSPHL-A in FIG. 14), while another utilizes the exons 1, 2 and 4(PSPHL-B). We have also identified an insertion/deletion polymorphism atthe PSPHL locus. The deleted genomic region spans more than 30 kb,including the promoter region and the exons 1, 2 and 3 of PSPHL gene.This genetic variance explains the present/absent pattern of the PSPHLexpression. An over-representation of the deletion allele resulting inthe absence of PSPHL expression increases susceptibility to BPD.

PSPHL and PSPH are highly homologous, but appear to be different genes,which are about 2OOkb apart from each other on chromosome 7p11.2 region.Especially, exons 2-4 of PSPHL are highly homologous to exons 4 and 8 ofPSPH gene. Predicted amino acid sequences of PSPH, PSPHL-A and PSPHL-Bare shown in FIG. 15. PSPHL-A and PSPHL-B share N-terminal 57 commonamino acids, transcribed from exons 1 and 2. PSPHL-A has uniqueC-terminal 36 amino acids, transcribed from exon3, while PSPHL-B hasunique C-terminal 17 amino acids, transcribed from exon 4. PSPH andPSPHL-A&B have 31 amino acids in common. The common amino acids locatesat the N-terminal end of PSPH and middle region (25th-56th amino acids)of PSPHL-A and B. The common region contains consensus phosphorylationsite of Na/K ATPase and casein kinase II phospholyration site. Based onthe similarity in the structure, PSPHL shares some function with PSPHgene.

PSPH is the rate limiting enzyme for serine synthesis. PSPH has haloaciddehalogenase-like hydrolase domain, which is responsible for theactivity. Greater than 90% of L-serine in brain is formed via thephosphorylated pathway. PSPH may be dimeric from of the enzyme with amonomeric molecular weight of 26 kDa. L-serine is converted tosphingomyelins and gangliosides, as well as L-glycine and D-serine, bothof which act as coagonist for NMDA receptor associated glycine bindingsite. L-glycine is also an agonist for strychnine-sensitive glycinereceptor (FIG. 16). PSPHL is involved in serine amino acid metabolicpathway, and may involved in other pathways as well.

Example 3 Post-Natal Injection of FGF2

This Example shows that neonatal administration of FGF-2 affectslong-term alterations in hippocampal volume, emotional reactivity andlearning and memory. Sprague-Dawley rats were injected with eithervehicle or FGF-2 (20 ng/g, s.c.) on postnatal day 2 (PD2). Three weeksafter injection we evaluated dentate gyrus volume and cell counts byNissl staining. We also assessed neurogenesis by BrdU and Ki-67immunohistochemistry at the 23 day time point. In adult rats, we testedlocomotor activity, anxiety behavior and learning and memory. Theanimals were sacrificed, and the brains collected for in situhybridization (FGF markers, stress markers). Results to date have shownthe following: FGF-2 injected rats exhibited a 10.5% increase in dentategyrus volume. The results show that FGF-2 significantly increasedlocomotor activity over controls in a novel environment. Increasedactivity in response to novelty has been associated with a host of othermeasures including decreased anxiety-like behavior. Furthermore, adultrats that received FGF-2 as neonates also performed significantly betterthan controls in the Morris water maze.

Example 4 FGF2 Expression

While evidence has linked growth factors such as BDNF to environmentalcomplexity (EC), responsiveness to stress, and antidepressant action,few studies focused on the role of the FGF system in emotionalreactivity. Recent data from our laboratory suggest that a singlepostnatal injection of FGF-2 significantly alters locomotor activity inresponse to a novel environment (Turner et al., SFN abstracts 2004).Since increased responsiveness to novelty is associated with decreasedanxiety-like behavior, we propose that FGF-2 may be correlated withother indices of emotionality. We tested the hypothesis that changes inemotionality associated with EC may be related to FGF-2 gene expressionin the hippocampus. Young adult male Sprague-Dawley rats were eitherexposed to a complex environment for 21 days or to standard cages.Following this treatment, rats were returned to standard cages for twoweeks. Brains were then processed for neurogenesis by BrdU and Ki-67immunohistochemistry. Another group of rats was tested in the elevatedplus-maze (EPM) and then sacrificed for in situ hybridization. Comparedto controls, EC rats showed significantly less anxiety-like behavior inthe EPM and exhibited a 23% increase in FGF-2 expression in thehippocampus. There was a significant positive correlation between FGF-2mRNA levels in hippocampal CA2 and time spent in the open arms of theEPM. Whether these results relate to levels of neurogenesis in thehippocampus is currently being determined. These findings are consistentwith our observations in human postmortem brains (Evans et al, SfNAbstracts 2004) showing that expression of several members of the FGFfamily is decreased in major depression. Together, these findingsimplicate the FGF system in emotionality and mood disorders.

Example 5

Cyclic Amp Signaling Pathway Genes Differentially Expressed in BPDand/or MDD Patients

Two independent cohorts A and B were analyzed separately in this study.Cohort A consisted of 22 subjects including 7 healthy control subjects,6 patients with BPD and 9 patients with MDD. Cohort B consisted of 12subjects including 5 MDD and 7 controls. All subjects in this study didnot have specific agonal conditions including hypoxia, coma, pyrexia,seizure, dehydration, hypoglycemia, multi-organ failure, skull fracture,ingestion of neurotoxic substances or prolonged agonal duration, whichis known to affect tissue pH, RNA integrity and gene expression profilein postmortem brain, and showed brain tissue pH of more than 6.5. Inorder to detect reliable gene expression differences between diagnosticgroups, we performed experimentally as well as biologically replicatedexperiments as follows. Experiment 1: Total RNA was extracted from AnCg,DLPFC and CB of the Cohort A, and purified with silica-based mini-spincolumns (Qiagen RNeasy Mini Kit, Valencia, Calif.). The oligonucleotidemicroarray experiments were carried out following the manufacturer'sprotocol (Affymetrix, Santa Clara, Calif.). For technical replication,each of RNA samples was run on Affymetrix U95Av2 GeneChips at twolaboratories. Experiment 2: For further technical replication, samplesfrom the 22 subjects from cohort A were reanalyzed in AnCg and DLPFCutilizing U133A GeneChips at two laboratories. Experiment 3: Samplesfrom the additional cohort B were analyzed on U133A GeneChips in AnCgand DLPFC at two laboratories. Signal intensity data was extracted withRobust Multi-array Average (RMA) for each probe set and each subject.Gene-wise Pearson's correlation coefficients between experimentalduplicates were calculated, and only the genes significantly correlatedbetween experimental duplicates were considered to be reliablydetectable genes, and subjected to the downstream analyses. For thesereliably detectable genes, mixed-model multivariate ANOVA analyses wereemployed utilizing Partek Pro 6.0 (Partek, St.Charles, Mo.) to adjustthe effect of the diagnostic classification (BPD, MDD, control) forpossible confounders, including site for experiment, experimental batch,and gender. Post hoc tests (least-squares difference) were run togenerate p value for the differences between case and control means, andfalse discovery rate multiple comparison corrections at the level ofaccepting 5% false positives was applied to each ANOVA result. When thep value passed false discovery rate multiple testing correction at thelevel of accepting 5% false positives and percent fold change exceeds20%, the genes were consider to be significantly differentiallyexpressed between case and control groups. Also, in order to evaluatemore subtle but consistent expression differences between case andcontrol groups, we also selected genes passed p value of 0.05 regardlessof FDR correction and % FC>10% on both experimental duplicates utilizingU95Av2 or U133A GeneChips.

FIG. 26A and Table 14 summarize cAMP signaling pathway related geneswhich were differentially expressed in anterior cingulate cortex (AnCg)of bipolar disorder (BPD) patients compared with controls. Among GPCRscoupled with G protein inhibitory subunit (Gi), which inhibits adenylatecyclase activity, neuropeptide Y receptor 1 (NPYR1) was significantlyincreased in AnCg of BPD. The ligand, neuropeptide Y was alsosignificantly increased in AnCg of BPD. Gi-linked metabotropic glutamatereceptor 3 (GRM3) was also increased in AnCg as well as dorsolateralprefrontal cortex (DLPFC) of BPD. Somatostatin (SST), a ligand forGi-coupled GPCR, was significantly increased in AnCg in our microarraydata.

Contrasted to the finding in AnCg, SST mRNA expression was decreased inDLPFC of BPD as well as major depressive disorder (MDD). Adrenergicbeta-1 receptor (ADRB1) was decreased by 13-18% in DLPFC of BPD,although the change did not reach the significant criteria (Table 17).Proenkephalin (PENK), a ligand for Gi-coupled GPCR, was not altered inAnCg and DLPFC of BPD and MDD, but significantly increased in CB of bothBPD and MDD.

Messenger RNA expression level of G protein alpha subunit inhibitorypeptide 1 (GNAI1) and phosphodiesterase 1A (PDE1A) were significantlyincreased in AnCg of BPD patients. Protein kinase A inhibitor alpha(PKIA) and cyclin dependent kinase 5 (CDK5), phosphodiesterase 8A(PDE8A) and protein phosphatase 1, catalytic subunit, alpha (PPP1CA) didnot reach significant criteria, but were increased by 10%-20% in AnCg ofBPD. Thus, mRNA expression of molecules suppressing cAMP concentrationand PKA activity were generally increased in BPD, while moleculesactivating cAMP signaling (Gs-coupled GPCR, Gs, adenylate cyclase,protein kinase A) did not show significant alteration at the transcriptlevel.

FIG. 26 and Table 14 summarize cAMP signaling pathway related geneswhich were differentially expressed in AnCg of MDD patients comparedwith controls. Gi-linked endothelial differentiation GPCR 1 (EDG1) wassignificantly decreased in AnCg of MDD. Regulator of G protein signaling20 (RGS20), phosphodiesterase 8A (PDE8A), and protein phosphatase 1regulatory subunit 3C (PPPlR3C) showed significantly lower expression inAnCg of MDD patients compared with controls. Expression levels of PDE8Aand PPP1R3C mRNAs were significantly lower also in DLPFC of MDD (Table15). Significant decrease in RGS20 expression in MDD was observed alsoin CB (Table 16). Thus, mRNA expression of molecules suppressing cAMPconcentration and PKA activity were generally decreased in MDD, whilethe molecules activating cAMP signaling did not show significantalteration at the transcript level.

Phosphatidylinositol Signaling Pathway

FIG. 26C and Table 14 summarize phosphatidylinositol signaling (PI)pathway related genes which were differentially expressed in AnCg of BPDpatients compared with controls. Gq-linked tachykinin (neuropeptide K)receptor 2 (TACR2) was significantly decreased in AnCg of BPD. MessengerRNA expression of inositol polyphosphate-1-phosphatase (INPP1) wassignificantly higher, while CDP-diacylglycerol synthase 1 (CDS 1), aregulatory subunit of class I phosphatidylinositol 3 kinase (PIK3R1) andprotein kinase C iota (PKCI) were significantly lower in AnCg of BPDpatients compared with control group. Inositol 1,4,5-trisphosphate3-kinase B (ITPKB) and catalytic beta subunit of class IIphosphatidylinositol 3 kinase (PIK3C2B) did not reach significancecriteria, but increased by 10%-20% in AnCg of BPD.

FIG. 26D and Table 14 summarize PI signaling pathway related genes whichwere differentially expressed in AnCg of MDD patients compared withcontrols. Gq-linked neurotensin receptor 2 (NTSR2) and endothelinreceptor type B (EDNRB) were significantly decreased in AnCg of MDD.Messenger RNA expression of inositol polyphosphate-5-phosphatase F(INPP5F) was significantly higher, while inositol 1,4,5-trisphosphate3-kinase B (ITPKB) and catalytic alpha subunit of class IIphosphatidylinositol 3 kinase (PIK3C2A) were significantly lower in AnCgof MDD compared with control. Inositol polyphosphate-5-phosphatase A(INPP5A), protein kinase C beta 1 (PKCB 1) and inositol1,4,5-triphosphate receptor type 1 (ITPR1) did not reach thesignificance criteria, but increased by 10-20% in AnCg of MDD patients.Significant decrease in ITPKB mRNA expression was observed also in DLPFCof MDD (Table 15). Neither G protein alpha q subunit nor phospholipase Cbeta mRNAs were altered in any of the brain regions of the disordergroups.

Other G Protein-Coupled Receptors

Among all GPCRs, the most consistent differential expression patternsthroughout our experiments were observed in G protein-coupled receptorfamily C, group 5, member B (GPRC5B) and G protein-coupled receptor 37(GPR37). GPRC5B was significantly increased in AnCg and DLPFC of BPD.GPRC5B was significantly decreased in AnCg, DLPFC and CB of MDDpatients. A significant decrease of GPRC5B in AnCg and DLPFC of MDDpatients was replicated by the experiments utilizing another independentcohort B. GPR37 was also significantly increased in AnCg of BPD, andsignificantly decreased in AnCg, DLPFC and CB of MDD.

Quantitative RT-PCR

For further technical evaluation of the microarray data, we evaluatedmRNA expression levels by real-time quantitative reverse transcriptasePCR (qRT-PCR) for the following 7 genes, in anterior cingulate cortex(AnCg): Somatostatin (SST), neuropeptide Y (NPY), G protein-coupledreceptor C-5-B (GPRC5B), G protein-coupled receptor 37 (GPR37),regulator of G-protein signaling 20 (RGS20), inositolpolyphosphate-1-phosphatase (INPP1) and protein phosphatase 1 regulatorysubunit 3C(PPPIR3C).

In consistent with microarray data, qRT-PCR data showed that mRNAexpressions of neuropeptide Y (NPY), G protein-coupled receptor C-5-B(GPRC5B), G protein-coupled receptor 37 (GPR37), inositolpolyphosphate-1-phosphatase (INPP1) were significantly increased in AnCgof BPD, and expression level of GPRC5B, GPR37, regulator of G-proteinsignaling 20 (RGS20) and protein phosphatase 1 regulatory subunit 3C(PPP1R3C) were significantly decreased in the AnCg of MDD group. Whilesomatostatin (SST) mRNA expression was increased in AnCg of BPD in bothmicroarray experimental duplicates utilizing U95Av2 and U133A, thefinding was not replicated by qRT-PCR (Table 17).

In Situ Hybridization

We performed in situ hybridization for GPR37 using. GPR37 mRNA ispreferentially expressed in subcortical white matter. GPR37 expressionin the deeper layers (V-VI) is relatively higher than the superficiallayers (I-II). GPR37 mRNA expression in subcortical white matter washigher in AnCg of the BPD subjects compared to the control subjects.GPR37 mRNA expression was rarely detected in AnCg of the MDD subjectsanalyzed. FIG. 27 shows the dysregulation of genes involved in cAMP- andphosphatidylinositol signaling pathways in brain tissue from patientswith BPD and MDD.

Gene Expression Changes in Amygdala, Hippocampus, Nucleus Accumbens ofBipolar Disorder and Major Depressive Disorder.

We applied the same experimental design on amygdala, hippocampus andnucleus accumbens of BPD and MDD. Table 18 summarizes genes which aredifferentially expressed in amygdala, hippocampus and nucleus accumbensof BPD patients. Table 19 summarizes genes differentially expressed inthe three brain regions of MDD.

Example 6

This Example shows gene dysregulation in pathways related toMitochondria, Proteasome, Apoptosis, and Chaperone in Mood Disorder.Three brain regions were studied: AnCg, Cerebellum, and DLPFC. Theresults are compiled in Tables 20-22.

Example 7

NCAM1 Association with Bipolar Disorder and Schizophrenia and SpliceVariants of NCAM1.

SNP and sample selection: Genomic DNA (gDNA) was extracted from humanpostmortem brain cerebellum tissue. Primers were designed for SNP 9 andthen tested via PCR to determine correct band size. Using the SNP 9primers, gDNA of 40 cases (20 controls, 9 BPDs and 11 MDDs) wassequenced with both the forward and reverse primers. The SNPs werelocated in exons a, b and c. SNPs b and c are intronic and found justbefore exon ‘b’ (7 bps upstream) and ‘c’ (12 bps upstream) respectively.Exon ‘a’ did not have a SNP in close proximity.

The genotypes were collected on an additional 26 bipolar genomic DNAsamples extracted from lymphocytes from the National Institute of MentalHealth (NIMH) for all 4 SNPs: SNP 6, SNP 9, SNP b and SNP c (see FIG.26). A third cohort was genotyped consisting of the Stanley Foundation105 dorsalateral prefrontal cortex (DLPFC) microarray samples (n=35controls, n=35 bipolar disorder, n=35 schizophrenia) (Table 24). TheStanley samples were genotyped for SNP 9 and SNP b. For final analysis,the three groups of bipolar cases were combined and three control groupswere merged and used for statistical comparisons of SNP 9 and SNP b. Theresults show an association of SNP 9 and SNP b haplotype with bipolardisorder and schizophrenia.

Genotype X Diagnosis Interaction for NCAM1 Splice Variants.

The splice variants are alternative splicing combinations of 3mini-exons (a,b,c) with the fourth SEC exon are shown in FIG. 30. Twomood disorders were tested (Bipolar Disorder, Type I and MajorDepressive Disorder, Recurrent) and both showed differences in NCAM1splice variants in the DLPFC.

The present data relates NCAM1 polymorphic variation to bipolar disorderand splice variations in mRNA occurring near the polymorphisms. Agenotypic association between SNP b in NCAM 1 and bipolar disorder and asuggestive association of SNP 9 with schizophrenia were found. Three ofthe two marker haplotypes for SNP 9 and SNP b, CT, C(T/C), and(C/A)(T/C) display varying frequency distribution between bipolar andcontrols. Schizophrenia and controls show differences in frequencydistribution in four of the two marker haplotypes of SNP 9 and SNP b,CT, C(T/C), (C/A)(T/C) and (C/A)C. Bipolar disorder differs fromschizophrenia for SNP 9 and SNP b by haplotype frequency differences.SNP b and SNP 9 are not in LD and they are individually related toschizophrenia (SNP 9) and bipolar disorder (SNP b).

The splice variant evidence for SNP 9 and b confirm that each SNP can beassociated with differences in SEC exon splicing, thus providing somedifferential mechanisms for release of NCAM1 in the brain. We observednotable differences between polymorphisms in NCAM1 and the relativeisoform variants of the SEC exon which can lead to truncation andsecretion of NCAM1 in the brain. This finding concerning the differencein splice variant relative amounts as a function of certain genotypeswas shown in three of the four SNPs where at least one genotype showed adifference in the amount of SEC by splice variant. This evidencesuggests that the amount of SEC in brain is not regulated by just onegenotype. Since the haplotypes composed of SNP 9 and SNP b aresignificantly different between controls and bipolar and betweencontrols and schizophrenia this may support the observation ofdifferential splicing patterns of the SEC exon found across manysamples. Additionally, SNP 9 and SNP b are not in LD and thus theindividual associations in schizophrenia and bipolar with these SNPsalso may be transmitted through differential splicing patterns. The SECexon was clearly regulated by certain combinations of mini-exons. Wehave identified discrete splice variants that can be further studied andare perhaps associated with regulatory intronic SNPs.

Example 8

Lithium has long been the drug of choice for treating manic-depressiveillness (manic-depression; bipolar affective disorder, BPD). ThisExample shows non-human primate genes which exhibit differentialexpression in response to treatment with lithium. The results haveimplications for understanding the mood stabilizing effects of lithiumin patients with manic depression.

Gene expression profiling was carried out on the anterior cingulatecortex (AnCg) using high-density oligonucleotide microarrays (AffymetrixGeneChips). We determined differential gene expression profiles ofpostmortem brains from lithium-treated healthy monkeys over those ofuntreated controls, and validated candidate genes against those known tobe lithium-responsive or disease-selective.

Some of the candidate genes that responded to chronic lithium treatmentwere the same as those found with changed expression levels inpostmortem brains of subjects with mood disorders. Our results show thatthe GSK3B signaling system is altered in BPD and that it is aphysiological target of lithium. The observed GSK3B signaling systemchange thus constitutes an endophenotype that is likely to be common toBPD and schizophrenia, notwithstanding their clinical and phenotypicdisparity. The results, by facilitating reconstruction of the geneticnetworks underlying BPD pathophysiology will facilitate the rationalmood stabilizers targeting the signal transduction network via GSK3.

Major depressive disorder (MDD) and bipolar affective disorder (BPD) aretwo most severe mood disorders. MDD is characterized by clinicaldepression, while BPD is marked by recurrent and dramatic swings ofemotional highs (mania) and lows (depression). For decades, lithiumcarbonate (Li₂CO₃, commonly known as “lithium”) has been the benchmarkmedication for mania (hyperactive, incoherent and delusional behavior).Lithium unlike other anti-manic treatment agents is unique in itsability to abort the manic condition and restore patient's balancedmental status. Although numerous hypotheses have been proposedaccounting for the neuro-protective properties of lithium, the precisemolecular mechanism(s) by which lithium elicits its “mood stabilizing”effects in manic-depressive patients remains obscure. We addressed thechallenge using a microarray strategy because it can permit simultaneousdetection of multiple lithium-responsive genes and pathways indrug-treated primates and direct comparison of the observed geneexpression changes with those found in postmortem brains from subjectswith BPD. Lithium carbonate suspension (Roxane Laboratories, Inc.,Columbus, Ohio) diluted in fruit juice was administered orally (18 mg/kgbody weight) to a targeted plasma level of 0.6 to 1.2 mgEq/mL. Theanimals received the drug twice a day for varying periods ranging from 4months to 1 year and 5 months to circumvent their tendency to spit thedrug out.

AnCg showed a total of 220 candidate transcripts (65 upregulated and 155down-regulated). The candidate genes from AnCg are listed in Table 28.Ontological annotations mapped candidate genes to several differentbiological processes and pathways, including GSK3B signaling system, aspredicted, in the AnCg.

AnCg involvement demonstrated in this study together with publishedreports of hippocampus involvement in lithium response implicates likelyinvolvement of the limbic system in mood disorders as well as in thedifferential gene expression elicited by chronic lithium treatment. Thepresent study also illuminates multiple interrelated functional networksof neuronal signaling pathways acting in unity with GSK3B as a pivotalfunctional switch regulating gene expression in behavioral diseases ofapparent disparate phenotypic diversity, BPD and SZ. The results showthat manipulating GSK3B could affect one or more of the inositoltriphosphate, NF-kB family, mitochondrial apoptosis, andubiquitin-proteasome pathways.

Example 9

V-Atpase Subunits as Gene Candidates of Interest for Major DepressiveDisorder (MDD).

Of the 14 V-ATPase subunits that we have interrogated with Affymicroarrays and Ulumina microarrays, 7 subunits (50%) are differentiallyexpressed (P<0.05) in hippocampal MDD versus control on either theAffymetrix or Illumina arrays. Three of the 7 subunits aredifferentially expressed in MDD hippocampus on both the Affymetrix andIllumina arrays (see Table 29). Two of the V-ATPase subunits are alsodifferentially expressed (P<0.05) in our Affy microarray study of monkeyhippocampus (i.e., Table 30, showing chronic social stress versusno-stress comparison). These findings demonstrate that drugs now beingdeveloped to inhibit V-ATPase in patients with cancer and osteoporosismay also prove useful as novel antidepressants.

The above examples are provided to illustrate the invention but not tolimit its scope. Other variants of the invention will be readilyapparent to one of ordinary skill in the art and are encompassed by theappended claims. All publications, databases, Genbank sequences,patents, and patent applications cited herein are hereby incorporated byreference. TABLE 1a Subject Data for Cohort A. AnCg DLPFC subject brain3′/5′ 3′/5′ ID gender age diagnosis pH PMI AnCg 18S/28S ratio ratio 1881M 69 BPD 6.91 11 0.68 1.36 1.21 2311 M 23 BPD 7.12 9 1.80 1.47 1.13 2466M 26 BPD 6.92 19 1.35 1.75 1.64 2566 F 56 BPD 6.83 29 1.05 1.48 1.343038 M 52 BPD 7.05 28 1.04 1.37 1.20 3241 M 59 BPD 6.99 16 1.38 1.331.17 averages for BPDs 47.5 6.97 18.6 1.22 1.46 1.28 2861 F 60 Ct 6.9924 1.25 2.07 1.80 3018 M 70 Ct 7.03 27 0.91 1.57 1.20 2169 M 18 Ct 6.9722 1.61 1.62 1.18 2316 M 58 Ct 7.02 26 1.27 1.47 1.27 2292 M 55 Ct 6.8915 1.45 1.29 1.18 2805 M 45 Ct 6.86 21 1.84 1.61 1.06 3196 M 44 Ct 6.8723 1.26 1.67 1.22 averages for 50 6.95 22.6 1.37 1.61 1.27 controls 2208F 72 MD 7.13 21 1.26 1.83 1.19 2267 M 19 MD 7.11 18 2.05 1.75 1.44 2315M 58 MD 6.93 24 1.34 1.52 1.31 3071 M 49 MD 7.00 31 1.58 1.44 1.25 3064M 46 MD 6.91 27 2.18 1.28 1.19 3031 M 49 MD 7.19 27 1.60 1.60 1.04 2944M 52 MD 6.82 16 1.37 1.91 1.43 3004 F 48 MD 6.95 37 1.31 1.81 1.20 3168M 39 MD 6.79 28 1.34 1.49 1.19 averages for MDDs 48.0 6.98 25.4 1.561.63 1.25

TABLE 1b Subject Data for Cohort B. AnCg DLPFC subject gen- brain AnCg3′/5′ 3′/5′ ID der age diagnosis pH PMI 18S/28S ratio ratio 3145 M 77 Ct6.62 7 3281 F 70 Ct 6.9 21 3516 M 41 Ct 7.01 23 3519 M 65 Ct 6.88 143523 M 40 Ct 7.07 37 3572 M 49 Ct 6.68 28 averages 57 6.86 21.67 forcontrols 3169 M 35 MD 7.04 25 3365 M 47 MD 7.25 29 3398 F 80 MD 6.68 153481 M 66 MD 7.05 32 averages 57 7.01 25.25 for MDDs

TABLE 2 Microarray data for all FGF transcripts reliably detected ineither DLPFC or AnCg and summary data for confirmation studies. DLPFCAnCg UniGene ID Transcript p-value direction p-value direction Hs.278954FGF1 <0.01^(‡,†) Decreased 0.01 Decreased Hs.284244 FGF2 NS <0.01*^(,‡)Decreased Hs.433252 FGF7 NS NS Hs.111 FGF9 <0.01 Increased <0.01*Increased Hs.343809 FGF12 NS <0.01* Increased Hs.6540 FGF13 NS NSHs.223851 FGF14 0.05 Increased NS Hs.748 FGFR1 NS Increased NS Hs.404081FGFR2 <0.01*^(,‡,†) Decreased <0.01*^(,‡) Decreased Hs.1420 FGFR3<0.01*^(,‡,†) Decreased <0.01* Decreased*Met FDR multiple testing correction at the level of accepting 5% falsepositives.^(‡)Observation was confirmed in an independent cohort of MDD andcontrol subjects given in Table 1b, meeting p-values of <0.05 in allcases indicated.^(†)Observation was confirmed by real-time PCR analysis with p < 0.05.NS = not significant.

TABLE 3 BPD Gene Bank UniGene ID Gene Symbol Gene Name RefSeq ID Acc.No. LocusLink Hs.407520 CHN2 chimerin (chimaerin) 2 NM_004067 U072231124 Hs.13351 LANCL1 LanC lantibiotic NM_006055 Y11395 10314 synthetasecomponent C-like 1 (bacterial) Hs.309090 SFRS7 splicing factor,NM_006276 L41887 6432 arginine/serinerich 7, 35 kDa Hs.7910 RYBP RING1and YY1 NM_012234 AL049940 23429 binding protein Hs.150101 LAMP1lysosomal-associated NM_005561 J04182 3916 membrane protein 1 Hs.90458SPTLC1 serine palmitoyl NM_006415 Y08685 10558 transferase, long chainbase subunit 1 Hs.406532 RPN2 ribophorin II NM_002951 AL031659 6185Hs.408883 SCN1B sodium channel, NM_001037 L10338 6324 voltage-gated,type I, beta Hs.91971 CGEF2 cAMP-regulated NM_007023 U78516 11069guanine nucleotide exchange factor II Hs.49117 — hypothetical protein —AL080093 — DKFZp564 N1662 Hs.84244 KCNB1 potassium volta NM_004 L028403745 DLPFC- DLPFC- UniGene ID Chromosome AnCg-BP AnCg-MD Criteria BP MDCriteria Hs.407520 Chr: 7p15.3 UP NC 2a, 3 Hs.13351 Chr: 2q33-q35 UP NC1, 2a UP NC 2a Hs.309090 Chr: 2p22.1 UP NC 1, 2a, 3 Hs.7910 Chr: 3p14.2UP NC 1, 2a, 3 Hs.150101 Chr: 13q34 UP NC 2a, 3 Hs.90458 Chr: 9q22.2 UPNC 1, 2a, 3 Hs.406532 Chr: 20q12-q13.1 UP NC 2a UP NC 1, 2a Hs.408883Chr: 19q13.1 DOWN NC 1, 3 Hs.91971 Chr: 2q31-q32 DOWN NC 1, 3 Hs.49117 —UP NC 1, 3 Hs.84244 Chr: 20q13.2 DOWN NC 1, 3

TABLE 4 MDD AnCg- AnCg- DLPFC- DLPFC- UniGene ID Gene Symbol Gene NameRefSeq ID Gene Bank Acc. No. LocusLink Chromosome BP MD Criteria BP MDCriteria Hs.5462 SLC4A4 solute carrier family 4, sodium NM_003759AF007216 8671 Chr: 4q21 NC DOWN 2b NC DOWN 3 bicarbonate cotransporter,member 4 Hs.44 PTN pleiotrophin (heparin binding NM_002825 M57399 5764Chr: 7q33-q34 NC DOWN 1, 2b growth factor 8, neurite growth- promotingfactor 1) Hs.144845 BBOX1 butyrobetaine (gamma), 2- NM_003986 AF0828688424 Chr: 11p14.2 NC DOWN 1, 2b, 3 oxoglutarate dioxygenase(gamma-butyrobetaine hydroxylase) 1 Hs.170133 FOXO1A forkhead box O1A(rhabdomyosarcoma) NM_002015 AF032885 2308 Chr: 13q14.1 NC DOWN 1, 2b NCDOWN 1, 3 Hs.62192 F3 coagulation factor III (thromboplastin, NM_001993J02931 2152 Chr: 1p22-p21 NC DOWN 1, 2b, 3 tissue factor) Hs.166994 FATFAT tumor suppressor homolog NM_005245 X87241 2195 Chr: 4q34-q35 NC DOWN1, 2b, 3 1 (Drosophila) Hs.82002 EDNRB endothelin receptor type BNM_000115 S57283 1910 13q22 NC DOWN 1, 2b NC DOWN 1, 2b, 3 Hs.403997VIL2 villin 2 (ezrin) NM_003379 X51521 7430 Chr: 6q25.2-q26 NC DOWN 1,2b Hs.8022 TU3A TU3A protein NM_007177 AF035283 11170 Chr: 3p21.1 NCDOWN 1, 2b Hs.356876 GPR125 G protein-coupled receptor XM_291111AK027494 166647 4p15.32-p15.31 NC DOWN 1, 2b, 3 125 Hs.450919 GPC5glypican 5 NM_004466 U66033 2262 Chr: 13q32 NC DOWN 1, 2b Hs.414151DAAM2 dishevelled associated activator NM_015345 AB002379 23500 Chr:6p21.1 NC DOWN 2b NC DOWN 3 of morphogenesis 2 Hs.172089 PORIMINpro-oncosis receptor inducing NM_052932 AL050161 114908 Chr: 11q22.1 NCDOWN 1, 3 membrane injury gene Hs.77546 ANKRD15 ankyrin repeat domain 15NM_015158 D79994 23189 Chr: 9p24.3 NC DOWN 1, 3 Hs.26208 COL16A1collagen, type XVI, alpha 1 NM_001856 M92642 1307 Chr: 1p35-p34 NC DOWN1, 3 Hs.434494 SYNJ2 synaptojanin 2 NM_003898 AF039945 8871 Chr: 6q25.3NC DOWN 1, 3 Hs.434418 MYT1L myelin transcription factor — AB02902923040 Chr: 2p25.3 NC UP 1, 3 1-like Hs.78748 RIMS3 regulating synapticmembrane — D87074 9783 Chr: 1pter-p22.2 NC UP 1, 3 exocytosis 3Hs.436987 ZNF288 zinc finger protein 288 NM_015642 AL050276 26137 Chr:3q13.2 NC DOWN 1 NC DOWN 1 Hs.391392 ID4 inhibitor of DNA binding 4,NM_001546 AL022726 3400 Chr: 6p22-p21 NC DOWN 1 dominant negativehelix-loop- helix protein Hs.109052 C14orf2 chromosome 14 open readingNM_004894 AF054175 9556 Chr: 14q32.33 NC UP 1 frame 2 Hs.33455 PADI2peptidyl arginine deiminase, NM_007365 AB023211 11240 Chr: 1p35.2-p35.1NC DOWN 1 type II Hs.438240 ZFYVE16 zinc finger, FYVE domain containingNM_014733 AB002303 9765 Chr: 5p15.2-q14.3 NC DOWN 1 16 Hs.75462 BTG2 BTGfamily, member 2 NM_006763 U72649 7832 Chr: 1q32 NC DOWN 1

TABLE 5 Growth Factor Pathway Genes UniGene ID Gene Symbol Gene NameRefSeq Transcript ID LocusLink Hs.433326 IGFBP2 insulin-like growthfactor NM_000597 3485 binding protein 2, 36 kDa Hs.16512 OGFRL1 opioidgrowth factor receptor- NM_024576 79627 like 1 Hs.799 DTR diphtheriatoxin receptor NM_001945 1839 (heparin-binding epidermal growth factor-like growth factor) Hs.105689 LTBP2 latent transforming growth NM_0004284053 factor beta binding protein 2 Hs.289019 LTBP3 latent transforminggrowth NM_021070 4054 factor beta binding protein 3 Hs.376032 PDGFAplatelet-derived growth NM_002607///NM_(—) 5154 factor alpha polypeptide033023 Hs.839 IGFALS insulin-like growth factor NM_004970 3483 bindingprotein, acid labile subunit Hs.342874 TGFBR3 transforming growthNM_003243 7049 factor, beta receptor III (betaglycan, 300 kDa) Hs.404081FGFR2 fibroblast growth factor NM_000141///NM_(—) 2263 receptor 2(bacteria- 022969///NM_022970/// expressed kinase, NM_022971///keratinocyte growth factor NM_022972/// receptor, craniofacialNM_022973///NM_(—) dysostosis 1, 022974///NM_022975/// Crouzon syndrome,NM_022976/// Pfeiffer syndrome, Jackson- NM_023028/// Weiss syndrome)NM_023029///NM_(—) 023030///NM_023031 Hs.433252 FGF7 fibroblast growthfactor NM_002009 2252 7 (keratinocyte growth factor) Hs.67896 OGFRopioid growth factor receptor NM_007346 11054 Hs.446350 TGFBRAP1transforming growth NM_004257 9392 factor, beta receptor associatedprotein 1 Hs.194208 FRS3 fibroblast growth factor NM_006653 10817receptor substrate 3 Hs.169300 TGFB2 transforming growth NM_003238 7042factor, beta 2 Hs.411881 GRB14 growth factor receptor- NM_004490 2888bound protein 14 Hs.1420 FGFR3 fibroblast growth factorNM_000142///NM_(—) 2261 receptor 3 (achondroplasia, 022965 thanatophoricdwarfism) Hs.450230 IGFBP3 insulin-like growth factor NM_000598 3486binding protein 3 Hs.308053 IGF1 insulin-like growth factor NM_0006183479 1 (somatomedin C) Hs.419124 MET met proto-oncogene NM_000245 4233(hepatocyte growth factor receptor) Hs.284244 FGF2 fibroblast growthfactor NM_002006 2247 2 (basic) Hs.76473 IGF2R insulin-like growthfactor NM_000876 3482 2 receptor Hs.410037 CTGF connective tissue growthNM_001901 1490 factor Hs.274313 IGFBP6 insulin-like growth factorNM_002178 3489 binding protein 6 Hs.111 FGF9 fibroblast growth factorNM_002010 2254 9 (glia-activating factor) Hs.380833 IGFBP5 insulin-likegrowth factor NM_000599 3488 binding protein 5 Hs.79095 EPS15 epidermalgrowth factor NM_001981 2060 receptor pathway substrate 15 Hs.2132 EPS8epidermal growth factor NM_004447 2059 receptor pathway substrate 8Hs.278954 FGF1 fibroblast growth factor NM_000800///NM_(—) 2246 1(acidic) 013394///NM_033136/// NM_033137 Hs.343809 FGF12 fibroblastgrowth factor NM_004113///NM_(—) 2257 12 021032 Hs.7768 FIBP fibroblastgrowth factor NM_004214///NM_(—) 9158 (acidic) intracellular 198897binding protein Hs.127842 HDGFRP3 hepatoma-derived growth NM_01607350810 factor, related protein 3 Hs.416959 HGS hepatocyte growth factor-NM_004712 9146 regulated tyrosine kinase substrate Hs.239176 IGF1Rinsulin-like growth factor NM_000875 3480 1 receptor Hs.435795 IGFBP7insulin-like growth factor NM_001553 3490 binding protein 7 Hs.439109NTRK2 neurotrophic tyrosine NM_006180 4915 kinase, receptor, type 2Hs.26776 NTRK3 neurotrophic tyrosine NM_002530 4916 kinase, receptor,type 3 Hs.43080 PDGFC platelet derived growth NM_016205 56034 factor CHs.44 PTN pleiotrophin (heparin NM_002825 5764 binding growth factor 8,neurite growth-promoting factor 1)/// pleiotrophin (heparin bindinggrowth factor 8, neurite growth-promoting factor 1) Hs.114360 TSC22transforming growth NM_006022///NM_(—) 8848 factor beta-stimulated183422 protein TSC-22 Hs.73793 VEGF vascular endothelial NM_003376 7422growth factor DLPFC MD DLPFC BP AnCg MD AnCg BP UniGene ID ChromosomalLocation % P direction direction direction direction Hs.433326 Chr:2q33-q34 25 up none up down Hs.16512 Chr: 6q13 28 down none none downHs.799 Chr: 5q23 38 none up none none Hs.105689 Chr: 14q24 42 none nonenone down Hs.289019 Chr: 11q12 43 none none none up Hs.376032 Chr: 7p2243 none none none down Hs.839 Chr: 16p13.3 48 none none none downHs.342874 Chr: 1p33-p32 54 none up none none Hs.404081 Chr: 10q26 55down none down up Hs.433252 Chr: 15q15-q21.1 59 none down none noneHs.67896 Chr: 20q13.3 59 none down none down Hs.446350 Chr: 2q12.2 61 upup none none Hs.194208 Chr: 6p21.1 64 none down up down Hs.169300 Chr:1q41 68 none none down none Hs.411881 Chr: 2q22-q24 69 none up up upHs.1420 Chr: 4p16.3 76 down none down none Hs.450230 Chr: 7p13-p12 76none down none down Hs.308053 Chr: 12q22-q23 81 down none down downHs.419124 Chr: 7q31 81 none up up none Hs.284244 Chr: 4q26-q27 84 noneup down none Hs.76473 Chr: 6q26 92 none none down down Hs.410037 Chr:6q23.1 93 down none none up Hs.274313 Chr: 12q13 94 none none up downHs.111 Chr: 13q11-q12 99 up up up none Hs.380833 Chr: 2q33-q36 99 downnone none down Hs.79095 Chr: 1p32 100 none none none up Hs.2132 Chr:12q23-q24 100 down up down none Hs.278954 Chr: 5q31 100 down none downnone Hs.343809 Chr: 3q28 100 none none none none Hs.7768 Chr: 11q13.1100 none none none up Hs.127842 Chr: 15q11.2 100 none none up noneHs.416959 Chr: 17q25 100 none none none up Hs.239176 Chr: 15q25-q26 100none none none down Hs.435795 Chr: 4q12 100 down down down noneHs.439109 Chr: 9q22.1 100 down none down none Hs.26776 Chr: 15q25 100none none none down Hs.43080 Chr: 4q32 100 none none none up Hs.44 Chr:7q33-q34/// 100 down none down none Chr: 7q33-q34 Hs.114360 Chr: 13q14100 none none up none Hs.73793 Chr: 6p12 100 down none down none

TABLE 6 GPCR Pathway Genes U95Av2 probe Gene Bank Acc. DLPFC- setUniGene ID Gene Symbol Gene Name RefSeq ID No. LocusLink ChromosomeAnCg-BP AnCg-MD BP DLPFC-MD CINP 38604_at Hs.1832 NPY neuropeptide YNM_000905 NM_000905 4852 Chr: 7p15.1 UP CINP 1430_at Hs.12409 SSTsomatostatin NM_001048 NM_001048 6750 Chr: 3q28 UP CINP 2083_at Hs.203CCKBR cholecystokinin NM_000731 BC000740 887 Chr: 11p15.4 UP B receptorCINP 39928_at Hs.512145 GRM3 glutamate receptor, NM_000840 NM_0008402913 Chr: 7q21.1-q21.2 UP UP metabotropic 3 CINP 32623_at Hs.167017GABBR1 gamma-aminobutyric NM_001470 NM_001470 2550 Chr: 6p21.31 UP acid(GABA) B receptor, 1 CINP 37095_r_(—) Hs.99855 FPRL1 formyl peptideNM_001462 M88107 2358 Chr: 19q13.3-q13.4 DOWN at receptor-like 1 CINP1198_at Hs.82002 EDNRB endothelin receptor NM_000115 M74921 1910 Chr:13q22 DOWN type B CINP 34297_at Hs.406094 GPR37 G protein-coupledNM_005302 T16257 2861 Chr: 7q31 UP DOWN UP DOWN receptor 37 (endothelinreceptor type B-like) CINP 40240_at Hs.448805 GPRC5B G protein-coupledNM_016235 AF202640 51704 Chr: 16p12 UP DOWN UP DOWN receptor, family C,group 5, member B CINP 38580_at Hs.469951 GNAQ guanine nucleotideNM_002072 U40038 2776 Chr: 9q21 UP UP binding protein (G protein), qpolypeptide CINP 38279_at Hs.437081 GNAZ guanine nucleotide NM_002073NM_002073 2781 Chr: 22q11.22 UP binding protein (G protein), alpha zpolypeptide CINP 38176_at Hs.155090 GNB5 guanine nucleotide NM_006578NM_016194 10681 Chr: 15q21.1 UP UP binding protein (G protein), beta 541086_at Hs.141492 RGS20 regulator of G- NM_003702 AF074979 8601 Chr:8q12.1 DOWN DOWN protein signalling 20 34272_at Hs.386726 RGS4 regulatorof G- NM_005613 AL514445 5999 Chr: 1q23.2 UP protein signalling 4 CINP36311_at Hs.416061 PDE1A phosphodiesterase NM_005019 NM_005019 5136 Chr:4 UP 1A, calmodulin- dependent 32645_at Hs.502577 PDE4DIPphosphodiesterase XM_380170 NM_022359 9659 Chr: 1q12 UP 4D interactingprotein (myomegalin) 37676_at Hs.78746 PDE8A phosphodiesterase NM_002605BE568219 5151 Chr: 15q25.2 DOWN 8A CINP 226_at Hs.280342 PRKAR1A proteinkinase, NM_002734 AL050038 5573 Chr: 17q23-q24 UP cAMP-dependent,regulatory, type I, alpha (tissue specific extinguisher 1) CINP 1383_atHs.512628 PPP2R2A protein phosphatase NM_002717 NM_002717 5520 Chr:8p21.1 UP UP 2 (formerly 2A), regulatory subunit B (PR 52), alphaisoform 39364_s_(—) Hs.303090 PPP1R3C protein phosphatase NM_005398N26005 5507 Chr: 10q23-q24 DOWN DOWN at 1, regulatory (inhibitor)subunit 3C 39780_at Hs.187543 PPP3CB protein phosphatase NM_021132NM_021132 5532 Chr: 10q21-q22 UP 3 (formerly 2B), catalytic subunit,beta isoform (calcineurin A beta) CINP 40704_at Hs.85701 PIK3CAphosphoinositide- NM_006218 NM_006218 5290 Chr: 3q26.3 DOWN 3-kinase,catalytic, alpha polypeptide CINP 33628_g_(—) Hs.426967 PIK3CDphosphoinositide- NM_005026 U86453 5293 Chr: 1p36.2 DOWN at 3-kinase,catalytic, delta polypeptide CINP 146_at Hs.154846 PIK4CBphosphatidylinositol NM_002651 NM_002651 5298 Chr: 1q21 UP 4-kinase,catalytic, beta polypeptide CINP 40217_s_(—) Hs.380684 CDS1CDP-diacylglycerol NM_001263 NM_001263 1040 Chr: 4q21.23 DOWN atsynthase (phosphatidate cytidylyltransferase) 1 CINP 656_at Hs.32309INPP1 inositol polyphosphate- NM_002194 NM_002194 3628 Chr: 2q32 UP1-phosphatase CINP 118_at Hs.2722 ITPKA inositol 1,4,5-trisphosphateNM_002220 NM_002220 3706 Chr: 15q14-q21 UP 3-kinase A 33508_at Hs.334575INPP4A inositol polyphosphate- NM_001566 AA355179 3631 Chr: 2q11.2 UP4-phosphatase, type I, 107 kDa 32779_s_(—) Hs.149900 ITPR1 inositol1,4,5-triphosphate NM_002222 NM_002222 3708 Chr: 3p26-p25 UP atreceptor, type 1 353_at Hs.7370 PITPNB phosphotidylinositol NM_012399AL031591 23760 Chr: 22q12.1 UP transfer protein, beta 1217_g_atHs.349845 PRKCB1 protein kinase NM_002738 NM_002738 5579 Chr: 16p11.2 UPUP C, beta 1 362_at Hs.407181 PRKCZ protein kinase NM_002744 NM_0027445590 Chr: 1p36.33-p36.2 UP C, zeta CINP 976_s_at Hs.324473 MAPK1mitogen-activated NM_002745 NM_002745 5594 Chr: 22q11.2 UP UP proteinkinase 1 CINP 1844_s_at Hs.132311 MAP2K1 mitogen-activated NM_002755AI571419 5604 Chr: 15q22.1-q22.33 UP UP protein kinase kinase 1 CINP1712_s_at Hs.134106 MAP2K4 mitogen-activated NM_003010 NM_003010 6416Chr: 17p11.2 UP UP protein kinase kinase 4 CINP 1557_at Hs.64056 PAK1p21/Cdc42/R NM_002576 U51120 5058 Chr: 11q13-q14 UP UP UP ac1-activatedkinase 1 (STE 20 homolog, y east) CINP 33073_at Hs.152663 PAK3 p21(CDKN1A)- NM_002578 AW085556 5063 Chr: Xq22.3-q23 UP UP UP UP activatedkinase 3 CINP 39736_at Hs.355832 CDC42 cell division cycle NM_001791NM_015858 998 Chr: 1p36.1 UP UP 42 (GTP binding protein, 25 kDa) CINP1590_s_at Hs.37003 HRAS v-Ha-ras Harvey NM_005343 NM_005343 3265 Chr:11p15.5 UP UP rat sarcoma viral oncogene homolog

TABLE 7 GROWTH FACTOR Gene MDD BPD UniGene ID Symbol Amy AnCg DLPFC HCnAcc Amy AnCg DLPFC HC nAcc Epidermal Growth Factor System Hs.419815 EGF−1.1 Hs.79095 EPS15 1.3 Hs.147176 EPS15R Hs.2132 EPS8 −1.2 Hs.799 DTR−1.1 Fibroblast Growth Factor System Hs.278954 FGF1 −1.2 −1.4 Hs.343809FGF12 1.5 1.5 Hs.6540 FGF13 1.5 1.5 Hs.223851 FGF14 1.5 1.3 1.4Hs.284244 FGF2 −1.4 −1.3 −1.4 −1.8 Hs.433252 FGF7 −1.1 Hs.111 FGF9 1.41.2 1.3 1.6 Hs.748 FGFR1 Hs.404081 FGFR2 −1.1 −1.3 −1.2 −1.3 Hs.1420FGFR3 −1.2 −1.4 −1.5 Hs.7768 FIBP 1.3 Hs.194208 FRS3 Insulin-Like GrowthFactor System Hs.308053 IGF1 Hs.239176 IGF1R −1.2 −1.3 Hs.76473 IGF2RHs.839 IGFALS Hs.433326 IGFBP2 1.4 Hs.450230 IGFBP3 −1.3 −1.4 Hs.1516IGFBP4 −1.6 Hs.380833 IGFBP5 −1.2 −1.2 Hs.274313 IGFBP6 Hs.435795 IGFBP7Neurotrophins Hs.439027 BDNF Hs.439109 NTRK2 −1.2 −1.4 −1.3 −1.3Hs.26776 NTRK3 Hs.194774 CNTFR Opioid Growth Factor System Hs.67896 OGFRHs.16512 OGFRL1 −1.2 −1.2 Platelet-Derived Growth Factor System Hs.1976PDGFB Hs.43080 PDGFC Hs.74615 PDGFRA −1.3 −1.3 −1.2 −1.3 Hs.307783PDGFRB Transforming Growth Factor System Hs.25195 EBAF Hs.435067 ECGF1Hs.170009 TGFA −1.1 Hs.169300 TGFB2 Hs.421496 TGFBI −1.9 Hs.82028 TGFBR2Hs.342874 TGFBR3 −1.3 Hs.446350 TGFBR AP1 Hs.114360 TSC22 Hs.241257LTBP1 −1.2 −1.1 Hs.105689 LTBP2 −1.2 Hs.289019 LTBP3 VascularEndothelial Growth Factor System Hs.73793 VEGF −1.4 Hs.78781 VEGFBHs.79141 VEGFC Other Growth Factors/Receptors Hs.89525 HDGF Hs.127842HDGFR 1.3 1.3 1.3 1.2 P3 Hs.44 PTN −1.2 Hs.270833 AREG Hs.410037 CTGFOther Growth Factor Receptor Signalling Proteins Hs.512118 GRB10Hs.411881 GRB14 Hs.411366 GRB2 1.1 Hs.416959 HGS 1.1 Hs.419124 MET

TABLE 8 GLU/GABA GABA/glutamate signaling genes in Mood Disorders - SFNgenes For IDF inclusion UniGene BPD MDD ID Gene Common name Locus AnCgDLPFC HC Amy AnCg DLPFC HC Amy GABAergic: GABA A receptor Hs.24969 alpha5 GABRA5 GABA (A) GABA-A-Ra5 15q11.2 1.58 1.64 1.58 receptor, alpha 5Hs.302352 beta 3 GABARB3 GABA (A) GABA-A-Rb3 15q11.2 1.54 receptor, beta3 Hs.7195 gamma 2 GABARG2 GABA (A) GABA-A-Rg2 5q3.1 1.58 1.64 1.59receptor, gamma 2 Glutamate receptor Hs.7117 ionotropic, GRIA1 IGluR15q31.1 1.18 AMPA1 Hs.512145 Glutamate GRM3 Glutamate mGluR3 7q21.1 1.221.32 receptor, receptor, metabotropic 3 metabotropic 3 Glutamatetransporters Hs.349088 Glutamate SLC1A2 Solute carrier GLT-1; 11p13 0.840.71 0.87 0.81 transporter, family 1 (glial EAAT2 Na+-dependent, highaffinity EAAT2 Hs.371369 Glutamate SLC1A3 Solute carrier GLAST; 5p130.65 Transporter, family 1 (glial EAAT1 Na+-dependent, high affinity -EAAT1 Glutamine synthetase Hs.442669 Glutamate- GLUL Glutamate-Glutamine 1q31 0.72 0.86 ammonia ammonia synthetase ligase ligase (glutsynthetase)GABA, gamma amino butyric acid; glut/glutamate, glutamic acid; MDD,major depressive disorder; BPD, bipolar disorderAnCg, anterior cingulate cortex; DLPFC, dorso-lateral prefrontal cortex;HC, hippocampus; Amy, amygdala.Numbers (Fold Change) in RED denote INCREASES, and BLUE the DECREASES

TABLE 9 Pathway Analysis Gene Category System Rank EASE score GeneCategory System Rank EASE score Dorsolareral Prefrontal Cortex BipolarDisorder Major Depressive Disorder PKC 1st 0.00495 Hs_GlutamateMetabolism GenMAPP 1st 0.338 Hs_G Protein Signaling GenMAPP 2nd 0.121Hs_G13 Signaling Pathway GenMAPP 2nd 0.387 Hs_Electron Transport ChainGenMAPP 3rd 0.212 G protein beta, gamma 3rd 0.478 Hs_Ribosomal ProteinsGenMAPP 4th 0.29 Hs_Peptide GPCRs GenMAPP 4th 0.566 Hs_Wnt signalingGenMAPP 5th 0.362 Hs_G Protein Signaling GenMAPP 5th 0.571 AnteriorCingulate Cortex Bipolar Disorder Major Depressive Disorder Hs_ElectronTransport Chain GenMAPP 1st 0.0972 GPCR-orphan 1st 0.0407 Hs_RibosomalProteins GenMAPP 2nd 0.102 Hs_Orphan GPCRs GenMAPP 2nd 0.0447GPCR-orphan 3rd 0.289 Hs_Electron Transport Chain GenMAPP 3rd 0.0677 PKA4th 0.368 GPCR 4th 0.189 Hs_Proteasome Degradation GenMAPP 5th 0.427 PIsignaling 5th 0.198 Amygdala Bipolar Disorder Major Depressive DisorderHs_Nuclear Receptors GenMAPP 1st 0.0826 Hs_Glycolysis andGluconeogenesis GenMAPP 1st 0.0022 Hs_Apoptosis GenMAPP 2nd 0.228Hs_Krebs-TCA Cycle GenMAPP 2nd 0.00447 GPCR-orphan 3rd 0.46 Hs_ElectronTransport Chain GenMAPP 3rd 0.0563 GPCR 4th 0.555 PI signaling 4th0.0846 Hs_Krebs-TCA Cycle GenMAPP 5th 0.61 Hs_G Protein SignalingGenMAPP 5th 0.154 Hippocampus Bipolar Disorder Major Depressive DisorderHs_Electron Transport Chain GenMAPP 1st 0.00000276 Hs_Electron TransportChain GenMAPP 1st 2.41E−07 Hs_Glycolysis and GenMAPP 2nd 0.00838Hs_Glycolysis and Gluconeogenesis GenMAPP 2nd 0.0059 GluconeogenesiscAMP signaling 3rd 0.134 Rn_Ribosomal Proteins GenMAPP 3rd 0.16 PKA 4th0.14 Hs_Krebs-TCA Cycle GenMAPP 4th 0.179 GPCR 5th 0.187 MAPK signaling5th 0.22 Arrray Data Large p-value(BP - FC(BP - NAME SYMBOL CategorySubcategory Control) Control) Dorsolateral Prefrontal Cortex BipolarDisorder vs Control UniGene Cluster Hs.458426 cholecystokinin CCK LigandLigand-neuropeptide 0.021 1.164 Hs.155090 guanine nucleotide bindingprotein (G GNB5 G protein GNB 0.025 1.210 protein), beta 5 beta, gammaHs.434387 protein kinase C, nu PRKCN PI signaling PKC 0.023 1.081Hs.496511 protein kinase C, iota PRKCI PI signaling PKC 0.048 1.184Hs.408049 protein kinase C, theta PRKCQ PI signaling PKC 0.046 1.104Hs.2890 protein kinase C, gamma PRKCG PI signaling PKC 0.032 0.757 MajorDepressive Disorder vs Control UniGene Cluster Hs.458426 cholecystokininCCK Ligand Ligand-neuropeptide 0.015 1.152 Hs.82002 endothelin receptortype B EDNRB GPCR GPCR-neuropeptide 0.000 0.550 Hs.184841 somatostatinreceptor 2 SSTR2 GPCR GPCR-neuropeptide 0.007 1.142 Hs.448805 Gprotein-coupled receptor, family C, GPRC5B GPCR GPCR-orphan 0.009 0.694group 5, member B Hs.6527 G protein-coupled receptor 56 GPR56 GPCRGPCR-orphan 0.010 0.790 Hs.155090 guanine nucleotide binding protein (GGNB5 G protein GNB 0.024 1.184 protein), beta 5 beta, gamma Hs.8107guanine nucleotide binding protein (G GNG12 G protein GNG 0.004 0.743protein), gamma 12 beta, gamma Hs.141492 regulator of G-proteinsignalling 20 RGS20 G protein RGS 0.007 0.582 regulator AnteriorCingulate Cortex Bipolar Disorder vs Control UniGene Cluster Hs.203cholecystokinin B receptor CCKBR GPCR GPCR-neuropeptide 0.019 1.215Hs.188 phosphodiesterase 4B, cAMP-specific PDE4B cAMP phosphodiesterase0.026 0.880 (phosphodiesterase E4 dunce homolog, signaling Drosophila)Hs.350631 A kinase (PRKA) anchor protein 13 AKAP13 cAMP PKA 0.019 0.887signaling Hs.440404 protein kinase, cAMP-dependent, PRKAR2A cAMP PKA0.007 0.954 regulatory, type II, alpha signaling Hs.183994 proteinphosphatase 1, catalytic subunit, PPP1CA cAMP PP related 0.004 1.152alpha isoform signaling Hs.435238 protein phosphatase 1, regulatoryPPP1R1A cAMP PP related 0.017 1.233 (inhibitor) subunit 1A signalingMajor Depressive Disorder vs Control UniGene Cluster Hs.82002 endothelinreceptor type B EDNRB GPCR GPCR-neuropeptide 0.001 0.565 Hs.203cholecystokinin B receptor CCKBR GPCR GPCR-neuropeptide 0.011 1.205Hs.406094 G protein-coupled receptor 37 GPR37 GPCR GPCR-orphan 0.0030.595 Hs.448805 G protein-coupled receptor, family C, GPRC5B GPCRGPCR-orphan 0.000 0.662 group 5, member B Hs.6527 G protein-coupledreceptor 56 GPR56 GPCR GPCR-orphan 0.002 0.787 Hs.46332 Gprotein-coupled receptor 6 GPR6 GPCR GPCR-orphan 0.042 1.249 Hs.160271 Gprotein-coupled receptor 48 GPR48 GPCR GPCR-orphan 0.000 0.713 Hs.166705G protein-coupled receptor 49 GPR49 GPCR GPCR-orphan 0.011 0.839Hs.198612 G protein-coupled receptor 51 GPR51 GPCR GPCR-orphan 0.0031.173 Hs.155090 guanine nucleotide binding protein (G GNB5 G protein GNB0.010 1.199 protein), beta 5 beta, gamma Hs.149900 inositol1,4,5-triphosphate receptor, type 1 ITPR1 PI signaling IP3 receptor0.003 1.227 Hs.153687 inositol polyphosphate-4-phosphatase, INPP4B PIsignaling Phosphatidylinositol 0.001 1.246 type II, 105 kDa metabolismHs.151408 phospholipase C, beta 4 PLCB4 PI signalingPhosphatidylinositol 0.005 1.215 metabolism Hs.52463 inositolpolyphosphate-5-phosphatase F INPP5F PI signaling Phosphatidylinositol0.003 1.181 metabolism Hs.158318 diacylglycerol kinase, beta 90 kDa DGKBPI signaling Phosphatidylinositol 0.024 1.192 metabolism Hs.249235phosphoinositide-3-kinase, class 2, PIK3C2A PI signalingPhosphatidylinositol 0.027 0.770 alpha polypeptide metabolism Hs.408063inositol polyphosphate-5-phosphatase, INPP5A PI signalingPhosphatidylinositol 0.011 1.126 40 kDa metabolism Hs.239818phosphoinositide-3-kinase, catalytic, PIK3CB PI signalingPhosphatidylinositol 0.021 1.084 beta polypeptide metabolism Hs.349845protein kinase C, beta 1 PRKCB1 PI signaling PKC 0.014 1.125 Hs.79000growth associated protein 43 GAP43 PI signaling PKC related 0.006 1.133Amygdala Bipolar Disorder vs Control Column ID Hs.12409 somatostatin SSTLigand Ligand-neuropeptide 0.011 1.672 Hs.46453 G protein-coupledreceptor 17 GPR17 GPCR GPCR-orphan 0.034 1.457 Hs.118552 likely orthologof rat GRP78-binding GBP GPCR GPCR-orphan 0.009 1.170 protein MajorDepressive Disorder vs Control UniGene Cluster Hs.22584 prodynorphinPDYN Ligand Ligand-neuropeptide 0.003 2.184 Hs.131138 neurotensinreceptor 2 NTSR2 GPCR GPCR-neuropeptide 0.001 0.684 Hs.82002 endothelinreceptor type B EDNRB GPCR GPCR-neuropeptide 0.005 0.706 Hs.46453 Gprotein-coupled receptor 17 GPR17 GPCR GPCR-orphan 0.003 0.661 Hs.6527 Gprotein-coupled receptor 56 GPR56 GPCR GPCR-orphan 0.000 0.781 Hs.448805G protein-coupled receptor, family C, GPRC5B GPCR GPCR-orphan 0.0390.870 group 5, member B Hs.155090 guanine nucleotide binding protein (GGNB5 G protein GNB 0.000 1.295 protein), beta 5 beta, gamma Hs.8107guanine nucleotide binding protein (G GNG12 G protein GNG 0.001 0.732protein), gamma 12 beta, gamma Hs.50612 guanine nucleotide bindingprotein (G GNA14 PI signaling GNA 0.007 0.691 protein), alpha 14Hs.149900 inositol 1,4,5-triphosphate receptor, type 1 ITPR1 PIsignaling IP3 receptor 0.003 1.454 Hs.158318 diacylglycerol kinase, beta90 kDa DGKB PI signaling Phosphatidylinositol 0.001 1.444 metabolismHs.78877 inositol 1,4,5-trisphosphate 3-kinase B ITPKB PI signalingPhosphatidylinositol 0.001 0.727 metabolism Hs.2722 inositol1,4,5-trisphosphate 3-kinase A ITPKA PI signaling Phosphatidylinositol0.011 1.461 metabolism Hs.408063 inositol polyphosphate-5-phosphatase,INPP5A PI signaling Phosphatidylinositol 0.003 1.358 40 kDa metabolismHs.429643 phospholipase C, beta 1 PLCB1 PI signalingPhosphatidylinositol 0.004 1.203 (phosphoinositide-specific) metabolismHs.249235 phosphoinositide-3-kinase, class 2, PIK3C2A PI signalingPhosphatidylinositol 0.013 0.782 alpha polypeptide metabolism Hs.52463inositol polyphosphate-5-phosphatase F INPP5F PI signalingPhosphatidylinositol 0.004 1.282 metabolism Hs.334575 inositolpolyphosphate-4-phosphatase, INPP4A PI signaling Phosphatidylinositol0.013 1.138 type I, 107 kDa metabolism Hs.25156 inositolpolyphosphate-5-phosphatase, INPP5E PI signaling Phosphatidylinositol0.014 0.914 72 kDa metabolism Hs.349845 protein kinase C, beta 1 PRKCB1PI signaling PKC 0.002 1.600 Hs.512640 protein kinase C substrate 80K-HPRKCSH PI signaling PKC 0.004 0.916 Hs.349611 protein kinase C, alphaPRKCA PI signaling PKC 0.005 0.923 Hippocampus Bipolar Disorder vsControl UniGene Cluster Hs.296341 CAP, adenylate cyclase-associated CAP2cAMP adenylate cyclase 0.035 1.396 protein, 2 (yeast) signaling relatedHs.13313 cAMP responsive element binding CREBL2 cAMP CRE 0.033 1.341protein-like 2 signaling Hs.203862 guanine nucleotide binding protein (GGNAI1 cAMP GNA 0.000 2.075 protein), alpha inhibiting activity signalingpolypeptide 1 Hs.157307 GNAS complex locus GNAS cAMP GNA 0.038 1.127signaling Hs.416467 phosphodiesterase 10A PDE10A cAMP phosphodiesterase0.001 0.921 signaling Hs.386791 phosphodiesterase 3A, cGMP-inhibitedPDE3A cAMP phosphodiesterase 0.005 0.790 signaling Hs.337616phosphodiesterase 3B, cGMP-inhibited PDE3B cAMP phosphodiesterase 0.0090.835 signaling Hs.43322 protein kinase, AMP-activated, alpha 1 PRKAA1cAMP PKA 0.001 0.880 catalytic subunit signaling Hs.350631 A kinase(PRKA) anchor protein 13 AKAP13 cAMP PKA 0.001 0.806 signaling Hs.280342protein kinase, cAMP-dependent, PRKAR1A cAMP PKA 0.003 1.569 regulatory,type I, alpha (tissue specific signaling extinguisher 1) Hs.156324protein kinase, cAMP-dependent, PRKACB cAMP PKA 0.012 1.418 catalytic,beta signaling Hs.3136 protein kinase, AMP-activated, gamma PRKAG1 cAMPPKA 0.014 1.225 1 non-catalytic subunit signaling Hs.433700 proteinkinase (cAMP-dependent, PKIA cAMP PKA related 0.014 1.385 catalytic)inhibitor alpha signaling Hs.79081 protein phosphatase 1, catalyticsubunit, PPP1CC cAMP PP related 0.001 1.426 gamma isoform signalingHs.267819 protein phosphatase 1, regulatory PPP1R2 cAMP PP related 0.0021.933 (inhibitor) subunit 2 signaling Hs.187543 protein phosphatase 3(formerly 2B), PPP3CB cAMP PP related 0.007 1.476 catalytic subunit,beta isoform signaling (calcineurin A beta) Hs.166071 cyclin-dependentkinase 5 CDK5 cAMP PP related 0.017 1.296 signaling Hs.21537 proteinphosphatase 1, catalytic subunit, PPP1CB cAMP PP related 0.005 1.334beta isoform signaling Hs.272458 protein phosphatase 3 (formerly 2B),PPP3CA cAMP PP related 0.017 1.357 catalytic subunit, alpha isoformsignaling (calcineurin A alpha) Hs.431156 protein phosphatase 2(formerly 2A), PPP2R1B cAMP PP related 0.017 0.927 regulatory subunit A(PR 65), beta signaling isoform Hs.380764 protein phosphatase 2(formerly 2A), PPP2R2B cAMP PP related 0.009 1.215 regulatory subunit B(PR 52), beta signaling isoform Hs.118244 protein phosphatase 2,regulatory PPP2R5D cAMP PP related 0.008 1.118 subunit B (B56), deltaisoform signaling Hs.356590 protein phosphatase 1, regulatory PPP1R8cAMP PP related 0.011 1.210 (inhibitor) subunit 8 signaling Hs.76556protein phosphatase 1, regulatory PPP1R15A cAMP PP related 0.045 0.828(inhibitor) subunit 15A signaling Major Depressive Disorder vs ControlUniGene Cluster Hs.234521 mitogen-activated protein kinase- MAPKAPK3MAPK 0.007 0.845 activated protein kinase 3 Hs.324473 mitogen-activatedprotein kinase 1 MAPK1 MAPK MAPK 0.007 1.612 signaling Hs.348446mitogen-activated protein kinase 9 MAPK9 MAPK 0.002 1.630 Hs.75074mitogen-activated protein kinase- MAPKAPK2 MAPK 0.006 0.872 activatedprotein kinase 2 Hs.271980 mitogen-activated protein kinase 6 MAPK6 MAPK0.004 1.471 Hs.25209 mitogen-activated protein kinase 10 MAPK10 MAPKMAPK 0.012 1.374 signaling Hs.134106 mitogen-activated protein kinasekinase 4 MAP2K4 MAPK MAPKK 0.004 1.657 signaling Hs.432453mitogen-activated protein kinase kinase MAP3K8 MAPKKK 0.004 0.807 kinase8 Hs.437214 mitogen-activated protein kinase kinase MAP3K9 MAPKKK 0.0081.162 kinase 9 Hs.28827 mitogen-activated protein kinase kinase MAP3K2MAPKKK 0.004 0.873 kinase 2 Hs.403927 mitogen-activated protein kinasekinase MAP3K7IP1 MAPKKK 0.041 0.847 kinase 7 interacting protein 1Hs.206097 related RAS viral (r-ras) oncogene RRAS2 MAPK RAS-MAPK 0.0020.863 homolog 2 signaling Hs.37003 v-Ha-ras Harvey rat sarcoma viralHRAS MAPK RAS-MAPK 0.008 1.196 oncogene homolog signaling Hs.412107v-Ki-ras2 Kirsten rat sarcoma 2 viral KRAS2 MAPK RAS-MAPK 0.013 1.451oncogene homolog signaling qRT-PCR Fold Change AnCg DLPFC Symbol UniGeneGene Name U133A qRT-PCR U133A qRT-PCR Bipolar Disorder vs Control CCKBRHs.203 Cholecystokinin B receptor 1.21{circumflex over ( )} 1.44** MajorDepressive Disorder vs Control EDNRB Hs.82002 Endothelin receptor type B0.57 0.63* 0.55{circumflex over ( )} 0.76 CCKBR Hs.203 cholecystokinin Breceptor 1.21 1.09 GPR37 Hs.406094 G protein-coupled receptor 370.59{circumflex over ( )} 0.74 GPRC5B Hs.448805 G protein-coupledreceptor C-5-B 0.66{circumflex over ( )} 0.65** 0.69{circumflex over( )} 0.85 GNB5 Hs.155090 G protein, beta 5 1.20 1.09 1.18{circumflexover ( )} 1.61** RGS20 Hs.141492 Regulator of G-protein signalling 200.58{circumflex over ( )} 0.70*e,cir  Microarray U133A, ANOVA p < 0.05*qRT-PCR, one tailed Student's t-test, p < 0.1**qRT-PCR, one tailed Student's t-test, p < 0.05

TABLE 10 Duplicate 1 Differential Expression 1 = No Mood And Region Hs.Unigene Value Rank Accession UniGene_ID LocusLink_ID Symbol DescriptionProbe_ID (BPDv C) AnCg Hs.20021_at −7.727057737 9 R17168 Hs.20021 6843VAMP1 VESICLE-ASSOCIATED MEMBRANE PROTEIN 1 (SYNAPTOBREVIN 1) Probe_ID(BPDv Hs.119316_at 7.019916677 17 AI075114 Hs.119316 5188 PET112LPET112-LIKE (YEAST) C) AnCg Probe_ID (BPDv Hs.194673_at 6.739939746 24AA954646 Hs.194673 8682 PEA15 PHOSPHOPROTEIN ENRICHED IN C) AnCgASTROCYTES 15 Probe_ID (BPDv C) AnCg Hs.356231_at −6.670345597 28AI038963 Hs.356231 79085 SLC25A23 SOLUTE CARRIER FAMILY 25(MITOCHONDRIAL CARRIER; PHOSPHATE CARRIER), MEMBER 23 Probe_ID (BPDvHs.438303_at 5.313202083 72 AA969386 Hs.438303 23395 LARS2 LEUCYL-TRNASYNTHETASE 2, C) AnCg MITOCHONDRIAL Probe_ID (BPDv Hs.109052_at5.019252834 103 AA865834 Hs.109052 9556 C14orf2 CHROMOSOME 14 OPEN C)AnCg READING FRAME 2 Probe_ID (BPDv Hs.76366_at 4.693419228 127 AA999694Hs.76366 572 BAD BCL2-ANTAGONIST OF CELL C) AnCg DEATH Probe_ID (BPDvHs.279939_at 4.582420323 138 AA977776 Hs.279939 23787 MTCH1MITOCHONDRIAL CARRIER C) AnCg HOMOLOG 1 (C. ELEGANS) Probe_ID (BPDvHs.74047_at 4.496465885 150 Hs.74047 C) AnCg Probe_ID (BPDv C) AnCgHs.3100_at 4.309487236 169 AA954213 Hs.3100 3735 KARS LYSYL-TRNASYNTHETASE Probe_ID (BPDv Hs.243491_at −4.224934266 183 Hs.243491 C)AnCg Probe_ID (BPDv Hs.3254_at 4.193592918 195 AA971301 Hs.3254 6150MRPL23 MITOCHONDRIAL RIBOSOMAL C) AnCg PROTEIN L23 Probe_ID (BPDvHs.177584_at 4.165654802 200 AA961910 Hs.177584 5019 OXCT1 3-OXOACID COATRANSFERASE 1 C) AnCg Probe_ID (BPDv Hs.14945_at −4.158983584 201 R17684Hs.14945 23305 ACSL6 ACYL-COA SYNTHETASE LONG- C) AnCg CHAIN FAMILYMEMBER 6 Probe_ID (BPDv Hs.511880_at −4.005278821 239 NM_000498Hs.511880 1585 CYP11B2 CYTOCHROME P450, FAMILY 11, C) AnCg SUBFAMILY B,POLYPEPTIDE 2 Probe_ID (BPDv C) AnCg Hs.149156_at 3.978596138 243AI148899 Hs.149156 2731 GLDC GLYCINE DEHYDROGENASE (DECARBOXYLATING;GLYCINE DECARBOXYLASE, GLYCINE CLEAVAGE SYSTEM PROTEIN P) Probe_ID (BPDvHs.433419_at 3.863300127 269 AA968887 Hs.433419 1327 COX4I1 CYTOCHROME COXIDASE C) AnCg SUBUNIT IV ISOFORM 1 Probe_ID (BPDv Hs.107476_at3.852124446 271 AA961439 Hs.107476 10632 ATP5L ATP SYNTHASE, H+ C) AnCgTRANSPORTING, MITOCHONDRIAL F0 COMPLEX, SUBUNIT G Probe_ID (BPDvHs.198269_at 3.834264322 274 AA970515 Hs.198269 4696 NDUFA3 NADHDEHYDROGENASE C) AnCg (UBIQUINONE) 1 ALPHA SUBCOMPLEX, 3, 9 KDA Probe_ID(BPDv Hs.75859_at 3.825790421 277 AA975309 Hs.75859 740 MRPL49MITOCHONDRIAL RIBOSOMAL C) AnCg PROTEIN L49 Probe_ID (BPDv Hs.144130_at−3.81230531 284 AA865892 Hs.144130 55186 FLJ10618 HYPOTHETICAL PROTEINC) AnCg FLJ10618 Probe_ID (BPDv Hs.3548_at 3.79318498 290 AA972489Hs.3548 4515 MTCP1 MATURE T-CELL C) AnCg PROLIFERATION 1 Probe_ID (BPDvC) AnCg Hs.7527_at 3.709781697 312 AA911794 Hs.7527 25996 DKFZP566E144SMALL FRAGMENT NUCLEASE Probe_ID (BPDv Hs.154672_at −3.613394429 338AA962299 Hs.154672 10797 MTHFD2 METHYLENE C) AnCg TETRAHYDROFOLATEDEHYDROGENASE (NAD+ DEPENDENT), METHENYLTETRAHYDROFOLATE CYCLOHYDROLASEProbe_ID (BPDv Hs.151573_at 3.581789697 347 AA905519 Hs.151573 1407 CRY1CRYPTOCHROME 1 C) AnCg (PHOTOLYASE-LIKE) Probe_ID (BPDv Hs.384944_at−3.45700168 390 R15701 Hs.384944 6648 SOD2 SUPEROXIDE DISMUTASE 2, C)AnCg MITOCHONDRIAL Probe_ID (BPDv Hs.8364_at 3.403571903 412 AI051630Hs.8364 5166 PDK4 PYRUVATE DEHYDROGENASE C) AnCg KINASE, ISOENZYME 4Probe_ID (BPDv C) AnCg Hs.139410_at −3.380539628 424 AI004719 Hs.1394101629 DBT DIHYDROLIPOAMIDE BRANCHED CHAIN TRANSACYLASE (E2 COMPONENT OFBRANCHED CHAIN KETO ACID DEHYDROGENASE COMPLEX; MAPLE SYRUP URINEDISEASE) Probe_ID (BPDv Hs.409430_at 3.374251626 427 AA954940 Hs.4094301716 DGUOK DEOXYGUANOSINE KINASE C) AnCg Probe_ID (BPDv Hs.300463_at3.35163141 436 Hs.300463 C) AnCg Probe_ID (BPDv Hs.211914_at 3.322183756446 R15290 Hs.211914 374291 NDUFS7 NADH DEHYDROGENASE C) AnCg(UBIQUINONE) FE-S PROTEIN 7, 20 KDA (NADH-COENZYME Q REDUCTASE) Probe_ID(MDD v Hs.3260_at −8.020507698 35 AA972181 Hs.3260 5663 PSEN1 PRESENILIN1 (ALZHEIMER C) AnCg DISEASE 3) Probe_ID (MDD v Hs.109052_at 6.38532974997 AA865834 Hs.109052 9556 C14orf2 CHROMOSOME 14 OPEN C) AnCg READINGFRAME 2 Probe_ID (MDD v Hs.75335_at −5.88132842 127 AA888620 Hs.75335145663 GATM GLYCINE C) AnCg AMIDINOTRANSFERASE (L- ARGININE:GLYCINEAMIDINOTRANSFERASE) Probe_ID (MDD v Hs.247309_at −5.878102056 128Hs.247309 C) AnCg Probe_ID (MDD v C) AnCg Hs.433419_at 5.758749759 136AA968887 Hs.433419 1327 COX4I1 CYTOCHROME C OXIDASE SUBUNIT IV ISOFORM 1Probe_ID (MDD v Hs.1342_at 5.348334665 175 AA902930 Hs.1342 1329 COX5BCYTOCHROME C OXIDASE C) AnCg SUBUNIT VB Probe_ID (MDD v Hs.49598_at5.345843386 176 AA969459 Hs.49598 23600 AMACR ALPHA-METHYLACYL-COA C)AnCg RACEMASE Probe_ID (MDD v Hs.353282_at 5.301845199 185 Hs.353282 C)AnCg Probe_ID (MDD v Hs.14945_at −5.275227195 190 R17684 Hs.14945 23305ACSL6 ACYL-COA SYNTHETASE LONG- C) AnCg CHAIN FAMILY MEMBER 6 Probe_ID(MDD v Hs.436405_at 5.186131647 200 AA976445 Hs.436405 3420 IDH3BISOCITRATE DEHYDROGENASE C) AnCg 3 (NAD+) BETA Probe_ID (MDD vHs.20021_at 4.974117426 234 R17168 Hs.20021 6843 VAMP1VESICLE-ASSOCIATED C) AnCg MEMBRANE PROTEIN 1 (SYNAPTOBREVIN 1) Probe_ID(MDD v C) AnCg Hs.182490_at 4.921605558 239 AA962471 Hs.182490 10128LRPPRC LEUCINE-RICH PPR-MOTIF CONTAINING Probe_ID (MDD v Hs.153792_at−4.902140124 243 AA905280 Hs.153792 4552 MTRR 5-METHYLTETRAHYDROFOLATE-C) AnCg HOMOCYSTEINE METHYLTRANSFERASE REDUCTASE Probe_ID (MDD vHs.3100_at 4.804444009 257 AA954213 Hs.3100 3735 KARS LYSYL-TRNASYNTHETASE C) AnCg Probe_ID (MDD v Hs.423404_at 4.802805566 259 AA975616Hs.423404 9167 COX7A2L CYTOCHROME C OXIDASE C) AnCg SUBUNIT VIIAPOLYPEPTIDE 2 LIKE Probe_ID (MDD v Hs.279939_at 4.722208682 269 AA977776Hs.279939 23787 MTCH1 MITOCHONDRIAL CARRIER C) AnCg HOMOLOG 1 (C.ELEGANS) Probe_ID (MDD v C) AnCg Hs.128410_at 4.581815327 287 AA886323Hs.128410 2744 GLS GLUTAMINASE Probe_ID (MDD v Hs.293970_at −4.511696936306 AA975064 Hs.293970 4329 ALDH6A1 ALDEHYDE DEHYDROGENASE 6 C) AnCgFAMILY, MEMBER A1 Probe_ID (MDD v Hs.528295_at −4.499310703 310 AI022321Hs.528295 10157 AASS AMINOADIPATE-SEMIALDEHYDE C) AnCg SYNTHASE Probe_ID(MDD v Hs.75760_at −4.363940471 336 R19294 Hs.75760 6342 SCP2 STEROLCARRIER PROTEIN 2 C) AnCg Probe_ID (MDD v Hs.9599_at −4.285016072 355AI032701 Hs.9599 10165 SLC25A13 SOLUTE CARRIER FAMILY 25, C) AnCg MEMBER13 (CITRIN) Probe_ID (MDD v Hs.7744_at 4.058060577 409 AA954362 Hs.77444723 NDUFV1 NADH DEHYDROGENASE C) AnCg (UBIQUINONE) FLAVOPROTEIN 1, 51KDA Probe_ID (MDD v C) AnCg Hs.350702_at 4.051168637 410 AA968881Hs.350702 23479 ISCU IRON-SULFUR CLUSTER ASSEMBLY ENZYME Probe_ID (MDD vHs.77690_at −4.044194861 414 R14803 Hs.77690 5869 RAB5B RAB5B, MEMBERRAS C) AnCg ONCOGENE FAMILY Probe_ID (MDD v Hs.287518_at −3.967121349437 AA970122 Hs.287518 5414 PNUTL2 PEANUT-LIKE 2 (DROSOPHILA) C) AnCgProbe_ID (MDD v Hs.1342_at 8.751574623 7 AA902930 Hs.1342 1329 COX5BCYTOCHROME C OXIDASE C) DLPFC SUBUNIT VB Probe_ID (MDD v Hs.182490_at8.000187313 18 AA962471 Hs.182490 10128 LRPPRC LEUCINE-RICH PPR-MOTIF C)DLPFC CONTAINING Probe_ID (MDD v Hs.128410_at 7.058759677 48 AA886323Hs.128410 2744 GLS GLUTAMINASE C) DLPFC Probe_ID (MDD v Hs.353282_at6.886768262 54 Hs.353282 C) DLPFC Probe_ID (MDD v Hs.173554_at6.797907829 64 AA961851 Hs.173554 7385 UQCRC2 UBIQUINOL-CYTOCHROME C C)DLPFC REDUCTASE CORE PROTEIN II Probe_ID (MDD v Hs.405860_at 6.78903473466 AA961135 Hs.405860 4191 MDH2 MALATE DEHYDROGENASE 2, C) DLPFC NAD(MITOCHONDRIAL) Probe_ID (MDD v Hs.3100_at 6.757315126 70 AA954213Hs.3100 3735 KARS LYSYL-TRNA SYNTHETASE C) DLPFC Probe_ID (MDD v C)DLPFC Hs.505824_at 6.576861944 81 AI023273 Hs.505824 25813 CGI-51 CGI-51PROTEIN Probe_ID (MDD v Hs.81886_at 6.233700436 98 AA905726 Hs.81886 549AUH AU RNA BINDING C) DLPFC PROTEIN/ENOYL-COENZYME A HYDRATASE Probe_ID(MDD v Hs.279939_at 6.126403025 103 AA977776 Hs.279939 23787 MTCH1MITOCHONDRIAL CARRIER C) DLPFC HOMOLOG 1 (C. ELEGANS) Probe_ID (MDD vHs.290404_at 5.971266153 119 AA954185 Hs.290404 5250 SLC25A3 SOLUTECARRIER FAMILY 25 C) DLPFC (MITOCHONDRIAL CARRIER; PHOSPHATE CARRIER),MEMBER 3 Probe_ID (MDD v Hs.196270_at 5.880975299 124 AI126840 Hs.19627081034 MFTC MITOCHONDRIAL FOLATE C) DLPFC TRANSPORTER/CARRIER Probe_ID(MDD v Hs.350702_at 5.844647665 128 AA968881 Hs.350702 23479 ISCUIRON-SULFUR CLUSTER C) DLPFC ASSEMBLY ENZYME Probe_ID (MDD v C) DLPFCHs.62185_at 5.820175161 130 AA954490 Hs.62185 10479 SLC9A6 SOLUTECARRIER FAMILY 9 (SODIUM/HYDROGEN EXCHANGER), ISOFORM 6 Probe_ID (MDD vHs.194673_at 5.818156637 131 AA954646 Hs.194673 8682 PEA15PHOSPHOPROTEIN ENRICHED IN C) DLPFC ASTROCYTES 15 Probe_ID (MDD vHs.439510_at 5.725481617 147 AA989107 Hs.439510 10730 YME1L1 YME1-LIKE 1(S. CEREVISIAE) C) DLPFC Probe_ID (MDD v Hs.109052_at 5.710330465 150AA865834 Hs.109052 9556 C14orf2 CHROMOSOME 14 OPEN C) DLPFC READINGFRAME 2 Probe_ID (MDD v Hs.409140_at 5.639633997 156 AA864297 Hs.409140539 ATP5O ATP SYNTHASE, H+ C) DLPFC TRANSPORTING, MITOCHONDRIAL F1COMPLEX, O SUBUNIT (OLIGOMYCIN SENSITIVITY CONFERRING PROTEIN) Probe_ID(MDD v Hs.250616_at 5.60246391 159 Hs.250616 C) DLPFC Probe_ID (MDD vHs.182217_at 5.57828738 164 AA984684 Hs.182217 8803 SUCLA2 SUCCINATE-COALIGASE, ADP- C) DLPFC FORMING, BETA SUBUNIT Probe_ID (MDD v Hs.7744_at5.54184827 169 AA954362 Hs.7744 4723 NDUFV1 NADH DEHYDROGENASE C) DLPFC(UBIQUINONE) FLAVOPROTEIN 1, 51 KDA Probe_ID (MDD v Hs.436405_at5.39739172 196 AA976445 Hs.436405 3420 IDH3B ISOCITRATE DEHYDROGENASE C)DLPFC 3 (NAD+) BETA Probe_ID (MDD v Hs.126608_at 5.3276937 207 AA962235Hs.126608 2908 NR3C1 NUCLEAR RECEPTOR C) DLPFC SUBFAMILY 3, GROUP C,MEMBER 1 (GLUCOCORTICOID RECEPTOR) Probe_ID (MDD v Hs.2043_at5.280565636 214 AA977341 Hs.2043 291 SLC25A4 SOLUTE CARRIER FAMILY 25 C)DLPFC (MITOCHONDRIAL CARRIER; ADENINE NUCLEOTIDE TRANSLOCATOR), MEMBER 4Probe_ID (MDD v Hs.144130_at 5.2188642 224 AA865892 Hs.144130 55186FLJ10618 HYPOTHETICAL PROTEIN C) DLPFC FLJ10618 Probe_ID (MDD vHs.78614_at 5.189788976 230 Hs.78614 C) DLPFC Probe_ID (MDD vHs.20716_at 5.188149858 231 AI021900 Hs.20716 10440 TIMM17A TRANSLOCASEOF INNER C) DLPFC MITOCHONDRIAL MEMBRANE 17 HOMOLOG A (YEAST) Probe_ID(MDD v Hs.407860_at 5.099673885 245 AA973726 Hs.407860 4718 NDUFC2 NADHDEHYDROGENASE C) DLPFC (UBIQUINONE) 1, SUBCOMPLEX UNKNOWN, 2, 14.5 KDAProbe_ID (MDD v Hs.20021_at 5.093990486 246 R17168 Hs.20021 6843 VAMP1VESICLE-ASSOCIATED C) DLPFC MEMBRANE PROTEIN 1 (SYNAPTOBREVIN 1)Probe_ID (MDD v Hs.268016_at 5.077587148 250 AA987838 Hs.268016 64968MRPS6 MITOCHONDRIAL RIBOSOMAL C) DLPFC PROTEIN S6 Probe_ID (MDD vHs.44298_at 5.017621789 266 AI141870 Hs.44298 51373 MRPS17 MITOCHONDRIALRIBOSOMAL C) DLPFC PROTEIN S17 Probe_ID (MDD v Hs.19236_at 4.976913834281 AA888160 Hs.19236 4711 NDUFB5 NADH DEHYDROGENASE C) DLPFC(UBIQUINONE) 1 BETA SUBCOMPLEX, 5, 16 KDA Probe_ID (MDD v Hs.429_at4.87511346 311 BI761550 Hs.429 518 ATP5G3 ATP SYNTHASE, H+ C) DLPFCTRANSPORTING, MITOCHONDRIAL F0 COMPLEX, SUBUNIT C (SUBUNIT 9) ISOFORM 3Probe_ID (MDD v Hs.131273_at 4.855540013 318 AA978176 Hs.131273 4976OPA1 OPTIC ATROPHY 1 (AUTOSOMAL C) DLPFC DOMINANT) Probe_ID (MDD vHs.433419_at 4.837055096 325 AA968887 Hs.433419 1327 COX4I1 CYTOCHROME COXIDASE C) DLPFC SUBUNIT IV ISOFORM 1 Probe_ID (MDD v Hs.436988_at4.817176809 332 AI025620 Hs.436988 1353 COX11 COX11 HOMOLOG, C) DLPFCCYTOCHROME C OXIDASE ASSEMBLY PROTEIN (YEAST) Probe_ID (MDD vHs.119251_at 4.800384591 337 AA954171 Hs.119251 7384 UQCRC1UBIQUINOL-CYTOCHROME C C) DLPFC REDUCTASE CORE PROTEIN I Probe_ID (MDD vHs.37_at 4.766384912 340 AI139512 Hs.37 38 ACAT1 ACETYL-COENZYME A C)DLPFC ACETYLTRANSFERASE 1 (ACETOACETYL COENZYME A THIOLASE) Probe_ID(MDD v Hs.11866_at 4.718266874 353 AA974086 Hs.11866 10431 TIMM23TRANSLOCASE OF INNER C) DLPFC MITOCHONDRIAL MEMBRANE 23 HOMOLOG (YEAST)Probe_ID (MDD v Hs.444757_at 4.716048741 354 AA968467 Hs.444757 23095KIF1B KINESIN FAMILY MEMBER 1B C) DLPFC Probe_ID (MDD v Hs.5556_at4.68842541 358 AA961682 Hs.5556 4706 NDUFAB1 NADH DEHYDROGENASE C) DLPFC(UBIQUINONE) 1, ALPHA/BETA SUBCOMPLEX, 1, 8 KDA Probe_ID (MDD vHs.211571_at 4.682127722 362 AA923565 Hs.211571 3052 HCCS HOLOCYTOCHROMEC C) DLPFC SYNTHASE (CYTOCHROME C HEME-LYASE) Probe_ID (MDD vHs.289271_at 4.679567034 365 AA863409 Hs.289271 1537 CYC1 CYTOCHROME C-1C) DLPFC Probe_ID (MDD v Hs.184860_at 4.647024454 373 AA973406 Hs.18486057128 C6orf149 CHROMOSOME 6 OPEN C) DLPFC READING FRAME 149 Probe_ID(MDD v Hs.247309_at −4.631146258 374 Hs.247309 C) DLPFC Probe_ID (MDD vHs.76366_at 4.541868883 388 AA999694 Hs.76366 572 BAD BCL2-ANTAGONIST OFCELL C) DLPFC DEATH Probe_ID (MDD v Hs.184233_at 4.524597014 395AA961767 Hs.184233 3313 HSPA9B HEAT SHOCK 70 KDA PROTEIN 9B C) DLPFC(MORTALIN-2) Probe_ID (MDD v Hs.300463_at 4.491205579 403 Hs.300463 C)DLPFC Probe_ID (MDD v Hs.107476_at 4.487968916 405 AA961439 Hs.10747610632 ATP5L ATP SYNTHASE, H+ C) DLPFC TRANSPORTING, MITOCHONDRIAL F0COMPLEX, SUBUNIT G Probe_ID (MDD v Hs.43549_at 4.482655426 407 AA975374Hs.43549 55847 C10orf70 CHROMOSOME 10 OPEN C) DLPFC READING FRAME 70Probe_ID (MDD v Hs.161357_at 4.415481565 415 R14727 Hs.161357 5162 PDHBPYRUVATE DEHYDROGENASE C) DLPFC (LIPOAMIDE) BETA Probe_ID (MDD vHs.198269_at 4.313217236 434 AA970515 Hs.198269 4696 NDUFA3 NADHDEHYDROGENASE C) DLPFC (UBIQUINONE) 1 ALPHA SUBCOMPLEX, 3, 9 KDA SummaryMDD with Drecti Change 0 2 Probe_ID Hs.107476_at 3.852124446 271AA961439 Hs.107476 10632 ATP5L ATP SYNTHASE, H+ (BPDv C) TRANSPORTING,AnCg MITOCHONDRIAL F0 COMPLEX, SUBUNIT G 1 3 Probe_ID Hs.107476_at4.487968916 405 AA961439 Hs.107476 10632 ATP5L ATP SYNTHASE, H+ (MDD vTRANSPORTING, C) MITOCHONDRIAL F0 COMPLEX, DLPFC SUBUNIT G 0 4 Probe_IDHs.109052_at 5.019252834 103 AA865834 Hs.109052 9556 C14orf2 CHROMOSOME14 OPEN (BPDv C) READING FRAME 2 AnCg 0 5 Probe_ID Hs.109052_at6.385329749 97 AA865834 Hs.109052 9556 C14orf2 CHROMOSOME 14 OPEN (MDD vREADING FRAME 2 C) AnCg 1 6 Probe_ID Hs.109052_at 5.710330465 150AA865834 Hs.109052 9556 C14orf2 CHROMOSOME 14 OPEN (MDD v READING FRAME2 C) DLPFC 1 7 Probe_ID Hs.11866_at 4.718266874 353 AA974086 Hs.1186610431 TIMM23 TRANSLOCASE OF INNER (MDD v MITOCHONDRIAL MEMBRANE 23 C)HOMOLOG (YEAST) DLPFC 1 8 Probe_ID Hs.119251_at 4.800384591 337 AA954171Hs.119251 7384 UQCRC1 UBIQUINOL-CYTOCHROME C (MDD v REDUCTASE COREPROTEIN I C) DLPFC 1 9 Probe_ID Hs.119316_at 7.019916677 17 AI075114Hs.119316 5188 PET112L PET112-LIKE (YEAST) (BPDv C) AnCg 1 10 Probe_IDHs.126608_at 5.3276937 207 AA962235 Hs.126608 2908 NR3C1 NUCLEARRECEPTOR (MDD v SUBFAMILY 3, GROUP C, C) MEMBER 1 (GLUCOCORTICOID DLPFCRECEPTOR) 0 11 Probe_ID Hs.128410_at 4.581815327 287 AA886323 Hs.1284102744 GLS GLUTAMINASE (MDD v C) AnCg 1 12 Probe_ID Hs.128410_at7.058759677 48 AA886323 Hs.128410 2744 GLS GLUTAMINASE (MDD v C) DLPFC 113 Probe_ID Hs.131273_at 4.855540013 318 AA978176 Hs.131273 4976 OPA1OPTIC ATROPHY 1 (AUTOSOMAL (MDD v DOMINANT) C) DLPFC 0 14 Probe_IDHs.1342_at 5.348334665 175 AA902930 Hs.1342 1329 COX5B CYTOCHROME COXIDASE (MDD v SUBUNIT VB C) AnCg 1 15 Probe_ID Hs.1342_at 8.751574623 7AA902930 Hs.1342 1329 COX5B CYTOCHROME C OXIDASE (MDD v SUBUNIT VB C)DLPFC 1 16 Probe_ID Hs.139410_at −3.380539628 424 AI004719 Hs.1394101629 DBT DIHYDROLIPOAMIDE BRANCHED (BPDv C) CHAIN TRANSACYLASE (E2 AnCgCOMPONENT OF BRANCHED CHAIN KETO ACID DEHYDROGENASE COMPLEX; MAPLE SYRUPURINE DISEASE) 0 17 Probe_ID Hs.144130_at −3.81230531 284 AA865892Hs.144130 55186 FLJ10618 HYPOTHETICAL PROTEIN (BPDv C) FLJ10618 AnCg 118 Probe_ID Hs.144130_at 5.2188642 224 AA865892 Hs.144130 55186 FLJ10618HYPOTHETICAL PROTEIN (MDD v FLJ10618 C) DLPFC 1 19 Probe_ID Hs.149156_at3.978596138 243 AI148899 Hs.149156 2731 GLDC GLYCINE DEHYDROGENASE (BPDvC) (DECARBOXYLATING; GLYCINE AnCg DECARBOXYLASE, GLYCINE CLEAVAGE SYSTEMPROTEIN P) 0 20 Probe_ID Hs.14945_at −4.158983584 201 R17684 Hs.1494523305 ACSL6 ACYL-COA SYNTHETASE LONG- (BPDv C) CHAIN FAMILY MEMBER 6AnCg 1 21 Probe_ID Hs.14945_at −5.275227195 190 R17684 Hs.14945 23305ACSL6 ACYL-COA SYNTHETASE LONG- (MDD v CHAIN FAMILY MEMBER 6 C) AnCg 122 Probe_ID Hs.151573_at 3.581789697 347 AA905519 Hs.151573 1407 CRY1CRYPTOCHROME 1 (BPDv C) (PHOTOLYASE-LIKE) AnCg 1 23 Probe_IDHs.153792_at −4.902140124 243 AA905280 Hs.153792 4552 MTRR5-METHYLTETRAHYDROFOLATE- (MDD v HOMOCYSTEINE C) AnCg METHYLTRANSFERASEREDUCTASE 1 24 Probe_ID Hs.154672_at −3.613394429 338 AA962299 Hs.15467210797 MTHFD2 METHYLENE (BPDv C) TETRAHYDROFOLATE AnCg DEHYDROGENASE(NAD+ DEPENDENT), METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE 1 25 Probe_IDHs.161357_at 4.415481565 415 R14727 Hs.161357 5162 PDHB PYRUVATEDEHYDROGENASE (MDD v (LIPOAMIDE) BETA C) DLPFC 1 26 Probe_IDHs.173554_at 6.797907829 64 AA961851 Hs.173554 7385 UQCRC2UBIQUINOL-CYTOCHROME C (MDD v REDUCTASE CORE PROTEIN II C) DLPFC 1 27Probe_ID Hs.177584_at 4.165654802 200 AA961910 Hs.177584 5019 OXCT13-OXOACID COA TRANSFERASE 1 (BPDv C) AnCg 1 28 Probe_ID Hs.182217_at5.57828738 164 AA984684 Hs.182217 8803 SUCLA2 SUCCINATE-COA LIGASE, ADP-(MDD v FORMING, BETA SUBUNIT C) DLPFC 0 29 Probe_ID Hs.182490_at4.921605558 239 AA962471 Hs.182490 10128 LRPPRC LEUCINE-RICH PPR-MOTIF(MDD v CONTAINING C) AnCg 1 30 Probe_ID Hs.182490_at 8.000187313 18AA962471 Hs.182490 10128 LRPPRC LEUCINE-RICH PPR-MOTIF (MDD v CONTAININGC) DLPFC 1 31 Probe_ID Hs.184233_at 4.524597014 395 AA961767 Hs.1842333313 HSPA9B HEAT SHOCK 70 KDA PROTEIN 9B (MDD v (MORTALIN-2) C) DLPFC 132 Probe_ID Hs.184860_at 4.647024454 373 AA973406 Hs.184860 57128C6orf149 CHROMOSOME 6 OPEN (MDD v READING FRAME 149 C) DLPFC 1 33Probe_ID Hs.19236_at 4.976913834 281 AA888160 Hs.19236 4711 NDUFB5 NADHDEHYDROGENASE (MDD v (UBIQUINONE) 1 BETA C) SUBCOMPLEX, 5, 16 KDA DLPFC0 34 Probe_ID Hs.194673_at 6.739939746 24 AA954646 Hs.194673 8682 PEA15PHOSPHOPROTEIN ENRICHED IN (BPDv C) ASTROCYTES 15 AnCg 1 35 Probe_IDHs.194673_at 5.818156637 131 AA954646 Hs.194673 8682 PEA15PHOSPHOPROTEIN ENRICHED IN (MDD v ASTROCYTES 15 C) DLPFC 1 36 Probe_IDHs.196270_at 5.880975299 124 AI126840 Hs.196270 81034 MFTC MITOCHONDRIALFOLATE (MDD v TRANSPORTER/CARRIER C) DLPFC 0 37 Probe_ID Hs.198269_at3.834264322 274 AA970515 Hs.198269 4696 NDUFA3 NADH DEHYDROGENASE (BPDvC) (UBIQUINONE) 1 ALPHA AnCg SUBCOMPLEX, 3, 9 KDA 1 38 Probe_IDHs.198269_at 4.313217236 434 AA970515 Hs.198269 4696 NDUFA3 NADHDEHYDROGENASE (MDD v (UBIQUINONE) 1 ALPHA C) SUBCOMPLEX, 3, 9 KDA DLPFC0 39 Probe_ID Hs.20021_at −7.727057737 9 R17168 Hs.20021 6843 VAMP1VESICLE-ASSOCIATED (BPDv C) MEMBRANE PROTEIN 1 AnCg (SYNAPTOBREVIN 1) 040 Probe_ID Hs.20021_at 4.974117426 234 R17168 Hs.20021 6843 VAMP1VESICLE-ASSOCIATED (MDD v MEMBRANE PROTEIN 1 C) AnCg (SYNAPTOBREVIN 1) 141 Probe_ID Hs.20021_at 5.093990486 246 R17168 Hs.20021 6843 VAMP1VESICLE-ASSOCIATED (MDD v MEMBRANE PROTEIN 1 C) (SYNAPTOBREVIN 1) DLPFC1 42 Probe_ID Hs.2043_at 5.280565636 214 AA977341 Hs.2043 291 SLC25A4SOLUTE CARRIER FAMILY 25 (MDD v (MITOCHONDRIAL CARRIER; C) ADENINENUCLEOTIDE DLPFC TRANSLOCATOR), MEMBER 4 1 43 Probe_ID Hs.20716_at5.188149858 231 AI021900 Hs.20716 10440 TIMM17A TRANSLOCASE OF INNER(MDD v MITOCHONDRIAL MEMBRANE 17 C) HOMOLOG A (YEAST) DLPFC 1 44Probe_ID Hs.211571_at 4.682127722 362 AA923565 Hs.211571 3052 HCCSHOLOCYTOCHROME C (MDD v SYNTHASE (CYTOCHROME C C) HEME-LYASE) DLPFC 1 45Probe_ID Hs.211914_at 3.322183756 446 R15290 Hs.211914 374291 NDUFS7NADH DEHYDROGENASE (BPDv C) (UBIQUINONE) FE-S PROTEIN 7, AnCg 20 KDA(NADH-COENZYME Q REDUCTASE) 1 46 Probe_ID Hs.243491_at −4.224934266 183Hs.243491 (BPDv C) AnCg 0 47 Probe_ID Hs.247309_at −5.878102056 128Hs.247309 (MDD v C) AnCg 1 48 Probe_ID Hs.247309_at −4.631146258 374Hs.247309 (MDD v C) DLPFC 1 49 Probe_ID Hs.250616_at 5.60246391 159Hs.250616 (MDD v C) DLPFC 1 50 Probe_ID Hs.268016_at 5.077587148 250AA987838 Hs.268016 64968 MRPS6 MITOCHONDRIAL RIBOSOMAL (MDD v PROTEIN S6C) DLPFC 0 51 Probe_ID Hs.279939_at 4.582420323 138 AA977776 Hs.27993923787 MTCH1 MITOCHONDRIAL CARRIER (BPDv C) HOMOLOG 1 (C. ELEGANS) AnCg 052 Probe_ID Hs.279939_at 4.722208682 269 AA977776 Hs.279939 23787 MTCH1MITOCHONDRIAL CARRIER (MDD v HOMOLOG 1 (C. ELEGANS) C) AnCg 1 53Probe_ID Hs.279939_at 6.126403025 103 AA977776 Hs.279939 23787 MTCH1MITOCHONDRIAL CARRIER (MDD v HOMOLOG 1 (C. ELEGANS) C) DLPFC 1 54Probe_ID Hs.287518_at −3.967121349 437 AA970122 Hs.287518 5414 PNUTL2PEANUT-LIKE 2 (DROSOPHILA) (MDD v C) AnCg 1 55 Probe_ID Hs.289271_at4.679567034 365 AA863409 Hs.289271 1537 CYC1 CYTOCHROME C-1 (MDD v C)DLPFC 1 56 Probe_ID Hs.290404_at 5.971266153 119 AA954185 Hs.290404 5250SLC25A3 SOLUTE CARRIER FAMILY 25 (MDD v (MITOCHONDRIAL CARRIER; C)PHOSPHATE CARRIER), MEMBER 3 DLPFC 1 57 Probe_ID Hs.293970_at−4.511696936 306 AA975064 Hs.293970 4329 ALDH6A1 ALDEHYDE DEHYDROGENASE6 (MDD v FAMILY, MEMBER A1 C) AnCg 0 58 Probe_ID Hs.300463_at 3.35163141436 Hs.300463 (BPDv C) AnCg 1 59 Probe_ID Hs.300463_at 4.491205579 403Hs.300463 (MDD v C) DLPFC 0 60 Probe_ID Hs.3100_at 4.309487236 169AA954213 Hs.3100 3735 KARS LYSYL-TRNA SYNTHETASE (BPDv C) AnCg 0 61Probe_ID Hs.3100_at 4.804444009 257 AA954213 Hs.3100 3735 KARSLYSYL-TRNA SYNTHETASE (MDD v C) AnCg 1 62 Probe_ID Hs.3100_at6.757315126 70 AA954213 Hs.3100 3735 KARS LYSYL-TRNA SYNTHETASE (MDD vC) DLPFC 1 63 Probe_ID Hs.3254_at 4.193592918 195 AA971301 Hs.3254 6150MRPL23 MITOCHONDRIAL RIBOSOMAL (BPDv C) PROTEIN L23 AnCg 1 64 Probe_IDHs.3260_at −8.020507698 35 AA972181 Hs.3260 5663 PSEN1 PRESENILIN 1(ALZHEIMER (MDD v DISEASE 3) C) AnCg 0 65 Probe_ID Hs.350702_at4.051168637 410 AA968881 Hs.350702 23479 ISCU IRON-SULFUR CLUSTER (MDD vASSEMBLY ENZYME C) AnCg 1 66 Probe_ID Hs.350702_at 5.844647665 128AA968881 Hs.350702 23479 ISCU IRON-SULFUR CLUSTER (MDD v ASSEMBLY ENZYMEC) DLPFC 0 67 Probe_ID Hs.353282_at 5.301845199 185 Hs.353282 (MDD v C)AnCg 1 68 Probe_ID Hs.353282_at 6.886768262 54 Hs.353282 (MDD v C) DLPFC1 69 Probe_ID Hs.3548_at 3.79318498 290 AA972489 Hs.3548 4515 MTCP1MATURE T-CELL (BPDv C) PROLIFERATION 1 AnCg 1 70 Probe_ID Hs.356231_at−6.670345597 28 AI038963 Hs.356231 79085 SLC25A23 SOLUTE CARRIER FAMILY25 (BPDv C) (MITOCHONDRIAL CARRIER; AnCg PHOSPHATE CARRIER), MEMBER 23 171 Probe_ID Hs.37_at 4.766384912 340 AI139512 Hs.37 38 ACAT1ACETYL-COENZYME A (MDD v ACETYLTRANSFERASE 1 C) (ACETOACETYL COENZYME ADLPFC THIOLASE) 1 72 Probe_ID Hs.384944_at −3.45700168 390 R15701Hs.384944 6648 SOD2 SUPEROXIDE DISMUTASE 2, (BPDv C) MITOCHONDRIAL AnCg1 73 Probe_ID Hs.405860_at 6.789034734 66 AA961135 Hs.405860 4191 MDH2MALATE DEHYDROGENASE 2, (MDD v NAD (MITOCHONDRIAL) C) DLPFC 1 74Probe_ID Hs.407860_at 5.099673885 245 AA973726 Hs.407860 4718 NDUFC2NADH DEHYDROGENASE (MDD v (UBIQUINONE) 1, SUBCOMPLEX C) UNKNOWN, 2, 14.5KDA DLPFC 1 75 Probe_ID Hs.409140_at 5.639633997 156 AA864297 Hs.409140539 ATP5O ATP SYNTHASE, H+ (MDD v TRANSPORTING, C) MITOCHONDRIAL F1COMPLEX, DLPFC O SUBUNIT (OLIGOMYCIN SENSITIVITY CONFERRING PROTEIN) 176 Probe_ID Hs.409430_at 3.374251626 427 AA954940 Hs.409430 1716 DGUOKDEOXYGUANOSINE KINASE (BPDv C) AnCg 1 77 Probe_ID Hs.423404_at4.802805566 259 AA975616 Hs.423404 9167 COX7A2L CYTOCHROME C OXIDASE(MDD v SUBUNIT VIIA POLYPEPTIDE 2 C) AnCg LIKE 1 78 Probe_ID Hs.429_at4.87511346 311 BI761550 Hs.429 518 ATP5G3 ATP SYNTHASE, H+ (MDD vTRANSPORTING, C) MITOCHONDRIAL F0 COMPLEX, DLPFC SUBUNIT C (SUBUNIT 9)ISOFORM 3 0 79 Probe_ID Hs.433419_at 3.863300127 269 AA968887 Hs.4334191327 COX4I1 CYTOCHROME C OXIDASE (BPDv C) SUBUNIT IV ISOFORM 1 AnCg 0 80Probe_ID Hs.433419_at 5.758749759 136 AA968887 Hs.433419 1327 COX4I1CYTOCHROME C OXIDASE (MDD v SUBUNIT IV ISOFORM 1 C) AnCg 1 81 Probe_IDHs.433419_at 4.837055096 325 AA968887 Hs.433419 1327 COX4I1 CYTOCHROME COXIDASE (MDD v SUBUNIT IV ISOFORM 1 C) DLPFC 1 82 Probe_ID Hs.43549_at4.482655426 407 AA975374 Hs.43549 55847 C10orf70 CHROMOSOME 10 OPEN (MDDv READING FRAME 70 C) DLPFC 0 83 Probe_ID Hs.436405_at 5.186131647 200AA976445 Hs.436405 3420 IDH3B ISOCITRATE DEHYDROGENASE (MDD v 3 (NAD+)BETA C) AnCg 1 84 Probe_ID Hs.436405_at 5.39739172 196 AA976445Hs.436405 3420 IDH3B ISOCITRATE DEHYDROGENASE (MDD v 3 (NAD+) BETA C)DLPFC 1 85 Probe_ID Hs.436988_at 4.817176809 332 AI025620 Hs.436988 1353COX11 COX11 HOMOLOG, (MDD v CYTOCHROME C OXIDASE C) ASSEMBLY PROTEIN(YEAST) DLPFC 1 86 Probe_ID Hs.438303_at 5.313202083 72 AA969386Hs.438303 23395 LARS2 LEUCYL-TRNA SYNTHETASE 2, (BPDv C) MITOCHONDRIALAnCg 1 87 Probe_ID Hs.439510_at 5.725481617 147 AA989107 Hs.439510 10730YME1L1 YME1-LIKE 1 (S. CEREVISIAE) (MDD v C) DLPFC 1 88 Probe_IDHs.44298_at 5.017621789 266 AI141870 Hs.44298 51373 MRPS17 MITOCHONDRIALRIBOSOMAL (MDD v PROTEIN S17 C) DLPFC 1 89 Probe_ID Hs.444757_at4.716048741 354 AA968467 Hs.444757 23095 KIF1B KINESIN FAMILY MEMBER 1B(MDD v C) DLPFC 1 90 Probe_ID Hs.49598_at 5.345843386 176 AA969459Hs.49598 23600 AMACR ALPHA-METHYLACYL-COA (MDD v RACEMASE C) AnCg 1 91Probe_ID Hs.505824_at 6.576861944 81 AI023273 Hs.505824 25813 CGI-51CGI-51 PROTEIN (MDD v C) DLPFC 1 92 Probe_ID Hs.511880_at −4.005278821239 NM_000498 Hs.511880 1585 CYP11B2 CYTOCHROME P450, FAMILY 11, (BPDvC) SUBFAMILY B, POLYPEPTIDE 2 AnCg 1 93 Probe_ID Hs.528295_at−4.499310703 310 AI022321 Hs.528295 10157 AASS AMINOADIPATE-SEMIALDEHYDE(MDD v SYNTHASE C) AnCg 1 94 Probe_ID Hs.5556_at 4.68842541 358 AA961682Hs.5556 4706 NDUFAB1 NADH DEHYDROGENASE (MDD v (UBIQUINONE) 1,ALPHA/BETA C) SUBCOMPLEX, 1, 8 KDA DLPFC 1 95 Probe_ID Hs.62185_at5.820175161 130 AA954490 Hs.62185 10479 SLC9A6 SOLUTE CARRIER FAMILY 9(MDD v (SODIUM/HYDROGEN C) EXCHANGER), ISOFORM 6 DLPFC 1 96 Probe_IDHs.74047_at 4.496465885 150 Hs.74047 (BPDv C) AnCg 1 97 Probe_IDHs.7527_at 3.709781697 312 AA911794 Hs.7527 25996 DKFZP566E144 SMALLFRAGMENT NUCLEASE (BPDv C) AnCg 1 98 Probe_ID Hs.75335_at −5.88132842127 AA888620 Hs.75335 145663 GATM GLYCINE (MDD v AMIDINOTRANSFERASE (L-C) AnCg ARGININE: GLYCINE AMIDINOTRANSFERASE) 1 99 Probe_ID Hs.75760_at−4.363940471 336 R19294 Hs.75760 6342 SCP2 STEROL CARRIER PROTEIN 2 (MDDv C) AnCg 1 100 Probe_ID Hs.75859_at 3.825790421 277 AA975309 Hs.75859740 MRPL49 MITOCHONDRIAL RIBOSOMAL (BPDv C) PROTEIN L49 AnCg 0 101Probe_ID Hs.76366_at 4.693419228 127 AA999694 Hs.76366 572 BADBCL2-ANTAGONIST OF CELL (BPDv C) DEATH AnCg 1 102 Probe_ID Hs.76366_at4.541868883 388 AA999694 Hs.76366 572 BAD BCL2-ANTAGONIST OF CELL (MDD vDEATH C) DLPFC 0 103 Probe_ID Hs.7744_at 4.058060577 409 AA954362Hs.7744 4723 NDUFV1 NADH DEHYDROGENASE (MDD v (UBIQUINONE) FLAVOPROTEIN1, C) AnCg 51 KDA 1 104 Probe_ID Hs.7744_at 5.54184827 169 AA954362Hs.7744 4723 NDUFV1 NADH DEHYDROGENASE (MDD v (UBIQUINONE) FLAVOPROTEIN1, C) 51 KDA DLPFC 1 105 Probe_ID Hs.77690_at −4.044194861 414 R14803Hs.77690 5869 RAB5B RAB5B, MEMBER RAS (MDD v ONCOGENE FAMILY C) AnCg 1106 Probe_ID Hs.78614_at 5.189788976 230 Hs.78614 (MDD v C) DLPFC 1 107Probe_ID Hs.81886_at 6.233700436 98 AA905726 Hs.81886 549 AUH AU RNABINDING (MDD v PROTEIN/ENOYL-COENZYME A C) HYDRATASE DLPFC 1 108Probe_ID Hs.8364_at 3.403571903 412 AI051630 Hs.8364 5166 PDK4 PYRUVATEDEHYDROGENASE (BPDv C) KINASE, ISOENZYME 4 AnCg 1 109 Probe_IDHs.9599_at −4.285016072 355 AI032701 Hs.9599 10165 SLC25A13 SOLUTECARRIER FAMILY 25, (MDD v MEMBER 13 (CITRIN) C) AnCg

TABLE 11 Genes dysregulated in MD, BP, and schizophrenia UniGene 1 IDprobe set Acc Name Symbol Direction of Change 2 Hs.282878 Hs.282878_atNM_021633 Kelch-like 12 KLHL12 DLPFC-BPD&MDD&SCZ-U (Drosophila) 3Hs.435039 Hs.435039_at NM_014914 Trinucleotide repeat CENTG2DLPFC-BPD&MDD&SCZ-U containing 17 4 Hs.530712 Hs.530712_at NM_017917Chromosome 14 open C14orf10 DLPFC-BPD&MDD&SCZ-U reading frame 10 5Hs.56294 Hs.56294_at NM_004794 RAB33A, member RAB33A DLPFC-BPD&MDD&SCZ-URAS oncogene family 6 Hs.21577 Hs.21577_at NM_005701 RNA, U transporter1 RNUT1 DLPFC-BPD&SCZ-U 7 Hs.274479 Hs.274479−_at NM_197972Non-metastatic cells 7, NME7 DLPFC-BPD&SCZ-U protein expressed in(nucleoside- diphosphate kinase) 8 Hs.368486 Hs.368486_at NM_001649Apical protein-like APXL DLPFC-BPD&SCZ-U (Xenopus laevis) 9 Hs.468415Hs.468415_at NM_002643 Phosphatidylinositol PIGF DLPFC-BPD&SCZ-U glycan,class F 10 Hs.471401 Hs.471401_at NM_004328 BCS1-like (yeast) BCS1LDLPFC-BPD&SCZ-U 11 Hs.502145 Hs.502145_at NM_006157 NEL-like 1 (chicken)NELL1 DLPFC-BPD&SCZ-U 12 Hs.514036 Hs.514036_at NM_006923 Stromalcell-derived SDF2 DLPFC-BPD&SCZ-U factor 2 13 Hs.532853 Hs.532853+_atNM_004146 NADH dehydrogenase NDUFB7 DLPFC-BPD&SCZ-U (ubiquinone) 1 betasubcomplex, 7, 18 kDa 14 Hs.111779 Hs.111779_at NM_003118 Secretedprotein, SPARC DLPFC-BPD&MDD&SCZ-D acidic, cysteine-rich (osteonectin)15 Hs.171695 Hs.171695_at NM_004417 Dual specificity DUSP1DLPFC-BPD&MDD&SCZ-D phosphatase 1 16 Hs.212838 Hs.212838−_at NM_000014Alpha-2-macroglobulin A2M DLPFC-BPD&MDD&SCZ-D 17 Hs.34560 Hs.34560−_atNM_005574 LIM domain only 2 LMO2 DLPFC-BPD&MDD&SCZ-D (rhombotin-like 1)18 Hs.347270 Hs.347270−_at NM_033554 Major HLA- DLPFC-BPD&MDD&SCZ-Dhistocompatibility DPA1 complex, class II, DP alpha 1 19 Hs.436568Hs.436568_at BC024272 CD74 antigen CD74 DLPFC-BPD&MDD&SCZ-D (invariantpolypeptide of major histocompatibility complex, class IIantigen-associated) 20 Hs.491582 Hs.491582_at NM_000931 Plasminogenactivator, PLAT DLPFC-BPD&MDD&SCZ-D tissue 21 Hs.534115 Hs.534115_atNM_006988 A disintegrin-like and ADAMTS1 DLPFC-BPD&MDD&SCZ-Dmetalloprotease (reprolysin type) with thrombospondin type 1 motif, 1 22Hs.17109 Hs.17109_at NM_004867 Integral membrane ITM2A DLPFC-BPD&SCZ-Dprotein 2A 23 Hs.485130 Hs.485130_at K01615 Major HLA- DLPFC-BPD&SCZ-Dhistocompatibility DPB1 complex, class II, DP beta 1 24 Hs.504877Hs.504877_at X69549 Rho GDP dissociation ARHGDIB DLPFC-BPD&SCZ-Dinhibitor (GDI) beta 25 Hs.520048 Hs.520048_at NM_019111 Major HLA-DRADLPFC-BPD&SCZ-D histocompatibility complex, class II, DR alpha

TABLE 12 Genes dysregulated in MD, BP, and schizophrenia Symbol NameUniGene ID AnCg DLPFC CB nAcc PTGDS Prostaglandin Hs.446429 CB-D nAcc-DPLAT Plasminogen activator, tissue Hs.491582 AnCg-D DLPFC-D ADAMTS1Disintegrin-like and metalloprotease Hs.534115 DLPFC-D nAcc-D

TABLE 13 Bipolar Disorder U95Av2 Cohort A UniGene GDB P % Fold IDAccession # Name Symbol Cytoband Value Change Monoamine MetabolismHs.370408 AL390148 Catechol-O- COMT 22q11.21-q11.23 <0.01 15.8methyltransfera Hs.46732 NM_000898 Monoamine MAOB Xp11.23 <0.01 15.9oxidase B Neuropeptide Ligand Hs.1832 BF680552 Neuropeptide Y NPY 7p15.1<0.01* 22.1 Hs.12409 BI918626 Somatostatin SST 3q28 <0.01* 29.0 Hs.1408BC053866 Endothelin 3 EDN3 20q13.2-q13.3 <0.01 −12.3 GPCRs Hs.519057L07615 Neuropeptide Y NPY1R 4q31.3-q32 receptor Y1 Hs.131138 NM_012344Neurotensin NTSR2 2p25.1 receptor 2 Hs.112621 BC041407 Metabotropic GRM37q21.1-q21.2 <0.01* 33.4 Glutamate receptor 3 Hs.88372 BC033742Tachykinin TACR2 10q11-q21 receptor 2 Hs.154210 BC018650 EndothelialEDG1 1p21 differentiation G- protein-coupled receptor 1 Hs.126667BC036034 Endothelial EDG2 9q31.3 <0.05 24.1 differentiation G-protein-coupled receptor 2 Hs.82002 NM_000115 Endothelin EDNRB 13q22receptor type B Hs.406094 BX649006 G protein-coupled GPR37 7q31 <0.01*53.1 receptor 37 Hs.513633 NM_201524 G protein-coupled GPR56 16q13receptor 56 Hs.148685 NM_016235 G protein-coupled GPRC5B 16p12 <0.01*38.4 receptor C-5-B Hs.99195 XM_291111 G protein-coupled GPR125 4p15.31receptor 125 G protein and Regulators Hs.134587 BC026326 G protein alphaGNAI1 7q21 inhibiting activity polypeptide 1 Hs.24950 NM_003617Regulator of G- RGS5 1q23.1 <0.01 −19.0 protein signalling 5 Hs.368733AK094559 Regulator of G- RGS20 8q12.1 protein signalling 20 Cyclic AMPSignaling Pathway Hs.416061 NM_005019 Phosphodiesterase PDE1A 2q32.1<0.01* 20.1 1A, calmodulin- dependent Hs.9333 NM_173457Phosphodiesterase PDE8A 15q25.3 <0.01 16.3 8A Hs.433700 NM_006823 cAMP-PKIA 8q21.11 <0.05 14.2 dependent Protein kinase inhibitor alphaHs.183994 AK098311 Protein PPP1CA 11q13 <0.01 13.1 phosphatase 1,catalytic subunit, alpha Hs.303090 BX537399 Protein PPP1R3C 10q23-q24phosphatase 1, regulatory subunit 3C Hs.166071 AK026533 Cyclin- CDK57q36 <0.01 10.5 dependent Phosphatidylinositol Signaling PathwayHs.374613 D26070 Inositol 1,4,5- ITPR1 3p26-p25 triphosphate receptor,type 1 Hs.460355 AL833252 Protein kinase PRKCB1 16p11.2 C, beta 1Hs.478199 NM_002740 Protein kinase PRKCI 0 <0.01* −29.5 C, iotaHs.444924 NM_001263 CDP- CDS1 4q21.23 <0.01* −29.5 diacylglycerolHs.32309 AK093560 synthase 1 INPP1 2q32 <0.01* 21.5 polyphosphate-1-phosphatase Hs.369755 NM_014937 Inositol INPP5F 10q26.11-q26.12polyphosphate- 5-phosphatase F Hs.528087 NM_002221 Inositol 1,4,5- ITPKB0 <0.01 14.8 trisphosphate 3- kinase B Hs.175343 BX648778Phosphoinositide- PIK3C2A 11p15.5-p14 3-kinase, class 2, alphapolypeptide Hs.497487 Y11312 Phosphoinositide- PIK3C2B 1q32 <0.01 16.63-kinase, class 2, beta polypeptide Hs.132225 NM_181523Phosphoinositide- PIK3R1 5q13.1 <0.01* −32.0 3-kinase, regulatorysubunit 1 Hs.467192 AK090488 Protein PPP2R1A 19q13.41 <0.01 12.1phosphatase 2, regulatory subunit A, alpha isoform Hs.146339 NM_002717Protein PPP2R2A 8p21.2 <0.01* 32.3 phosphatase 2, regulatory subunit B,alpha isoform Major Bipolar Depressive Disorder Disorder U133A U95Av2U133A U133A Cohort A Cohort A Cohort A Cohort B UniGene P % Fold P %Fold P % Fold P % Fold ID Value Change Value Change Value Change ValueChange Monoamine Metabolism Hs.370408 <0.01 11.5 Hs.46732 <0.01 18.9Neuropeptide Ligand Hs.1832 <0.01* 33.0 Hs.12409 <0.01* 22.1 Hs.1408<0.01 −10.0 GPCRs Hs.519057 <0.01* 24.4 <0.01* 21.9 <0.05 −17.7Hs.131138 <0.01 −13.9 <0.01 −18.6 <0.01* −24.7 Hs.112621 <0.01* 34.4Hs.88372 <0.01* −22.9 Hs.154210 <0.01 −19.7 <0.01* −21.2 <0.01 −10.4Hs.126667 <0.01 18.2 Hs.82002 <0.01* −31.2 <0.01 −15.9 Hs.406094 <0.01*38.3 <0.01* −53.5 <0.01* −40.5 <0.01* −27.0 Hs.513633 <0.01 −12.0 <0.01−15.9 <0.01 −14.9 Hs.148685 <0.01* 24.6 <0.01* −36.5 <0.01* −38.3 <0.01*−30.3 Hs.99195 <0.05 −14.1 <0.05 −11.5 G protein and RegulatorsHs.134587 <0.01* 40.4 Hs.24950 <0.01* −27.2 Hs.368733 <0.01 15.6 <0.01*−28.2 <0.01* −29.2 <0.01 −13.9 Cyclic AMP Signaling Pathway Hs.416061<0.01* 24.1 Hs.9333 <0.01 12.5 <0.01* −24.3 <0.01* −23.1 <0.01 −17.8Hs.433700 <0.01 16.6 Hs.183994 <0.01 16.8 Hs.303090 <0.01 −15.4 <0.01*−35.4 <0.01* −63.2 <0.01* −21.4 Hs.166071 <0.01 12.0Phosphatidylinositol Signaling Pathway Hs.374613 <0.05 13.0 <0.01 17.4Hs.460355 <0.01 14.8 <0.01 11.5 Hs.478199 Hs.444924 Hs.32309 <0.01* 24.9Hs.369755 <0.01* 21.8 Hs.528087 <0.05 11.5 <0.01 −12.7 <0.05 −12.3<0.01* −34.0 Hs.175343 <0.05 22.3 <0.05 −14.1 <0.01* −35.9 Hs.497487<0.01 14.8 Hs.132225 Hs.467192 <0.01 10.1 Hs.146339

TABLE 14 Bipolar Disorder U95Av2 Cohort A Name Symbol UniGene ID GDB Acc# G protein Cytoband P Value Monoamine Metabolism Catechol-O- COMTHs.370408 AL390148 22q11.21-q11.23 <0.01 methyltransferase MonoamineMAOB Hs.46732 NM_000898 Xp11.23 <0.01 oxidase B Ligand peptideNeuropeptide Y NPY Hs.1832 BF680552 Gi, Gq 7p15 <0.01* Somatostatin SSTHs.12409 BI918626 Gi 3q28 <0.01* Endothelin 3 EDN3 Hs.1408 BC053866 Gq20q13.2-q13.3 <0.01 GPCRs Neuropeptide Y NPY1R Hs.519057 L07615 Gi4q31-q32 receptor Y1 Tachykinin TACR2 Hs.88372 BC033742 Gq 10q11-q21receptor 2 Neurotensin NTSR2 Hs.131138 NM_012344 Gq 2p25.1 receptor 2Endothelin EDNRB Hs.82002 NM_000115 Gq 13q22 receptor type BMetabotropic GRM3 Hs.112621 BC041407 Gi 7q21 <0.01* Glutamate receptor 3Endothelial EDG1 Hs.154210 BC018650 Gi, G12 1p21 differentiation GPCR 1Endothelial EDG2 Hs.126667 BC036034 Gi, Gq, 9q31.3 <0.05 differentiationG12 GPCR 2 G protein-coupled GPR37 Hs.406094 BX649006 Unknown 7q31<0.01* receptor 37 G protein-coupled GPRC5B Hs.148685 NM_016235 Unknown16p12 <0.01* receptor C-5-B G protein-coupled GPR56 Hs.513633 NM_201524Unknown 16q13 receptor 56 G protein-coupled GPR125 Hs.99195 XM_291111Unknown 4p15 receptor 125 Cyclic AMP Signaling Pathway G protein alphaGNAI1 Hs.134587 BC026326 7q21 inhibiting activity 1 Regulator of G-RGS20 Hs.368733 AK094559 8q12 protein signalling 20 PhosphodiesterasePDE1A Hs.416061 NM_005019 2q32 <0.01* 1A Phosphodiesterase PDE8A Hs.9333NM_173457 15q25 <0.01 8A Protein kinase A PKIA Hs.433700 NM_006823 8q21<0.05 inhibitor alpha Cyclin-dependent CDK5 Hs.166071 AK026533 7q36<0.01 kinase 5 Protein PPP1CA Hs.183994 AK098311 11q13 <0.01 phosphatase1, catalytic alpha Protein PPP1R3C Hs.303090 BX537399 10q23-q24phosphatase 1, regulatory 3C Phosphatidylinositol Signaling PathwayInositol INPP5A Hs.523360 NM_005539 10q26 polyphosphate-5- phosphatase AInositol INPP5F Hs.369755 NM_014937 10q26 polyphosphate-5- phosphatase FInositol 1,4,5- ITPKB Hs.528087 NM_002221 1q41-q43 <0.01 trisphosphate3- kinase B Inositol INPP1 Hs.32309 AK093560 2q32 <0.01*polyphosphate-1- phosphatase CDP- CDS1 Hs.444924 NM_001263 4q21.23<0.01* diacylglycerol synthase 1 Phosphoinositide- PIK3C2A Hs.175343BX648778 11p15-p14 3-kinase catalytic 2A Phosphoinositide- PIK3C2BHs.497487 Y11312 1q32 <0.01 3-kinase catalytic 2B Phosphoinositide-PIK3R1 Hs.132225 NM_181523 5q13 <0.01* 3-kinase regulatory 1 Proteinkinase C PRKCI Hs.478199 NM_002740 3p25-q27 <0.01* iota Inositol 1,4,5-ITPR1 Hs.374613 D26070 3p26-p25 triphosphate receptor 1 Protein kinase CPRKCB1 Hs.460355 AL833252 16p11 beta 1 Bipolar Disorder Major DepressiveDisorder U95Av2 U133A U95Av2 U133A U133A Cohort A Cohort A Cohort ACohort A Cohort B Name % FC P Value % FC P Value % FC P Value % FC PValue % FC Monoamine Metabolism Catechol-O- 15.8 <0.01 11.5methyltransferase Monoamine 15.9 <0.01 18.9 oxidase B Ligand peptideNeuropeptide Y 22.1 <0.01* 33.0 Somatostatin 29.0 <0.01* 22.1 Endothelin3 −12.3 <0.01 −10.0 GPCRs Neuropeptide Y <0.01* 24.4 receptor Y1Tachykinin <0.01* −22.9 receptor 2 Neurotensin <0.01 −13.9 <0.01 −18.6<0.01* −24.7 receptor 2 Endothelin <0.01* −31.2 <0.01 −15.9 receptortype B Metabotropic 33.4 <0.01* 34.4 Glutamate receptor 3 Endothelial<0.01 −19.7 <0.01* −21.2 <0.01 −10.4 differentiation GPCR 1 Endothelial24.1 <0.01 18.2 differentiation GPCR 2 G protein-coupled 53.1 <0.01*38.3 <0.01* −53.5 <0.01* −40.5 <0.01* −27.0 receptor 37 Gprotein-coupled 38.4 <0.01* 24.6 <0.01* −36.5 <0.01* −38.3 <0.01* −30.3receptor C-5-B G protein-coupled <0.01 −12.0 <0.01 −15.9 <0.01 −14.9receptor 56 G protein-coupled <0.05 −14.1 <0.05 −11.5 receptor 125Cyclic AMP Signaling Pathway G protein alpha <0.01* 40.4 inhibitingactivity 1 Regulator of G- <0.01* −28.2 <0.01* −29.2 <0.01 −13.9 proteinsignalling 20 Phosphodiesterase 20.1 <0.01* 24.1 1A Phosphodiesterase16.3 <0.01 12.5 <0.01* −24.3 <0.01* −23.1 <0.01 −17.8 8A Protein kinaseA 14.2 <0.01 16.6 inhibitor alpha Cyclin-dependent 10.5 <0.01 12.0kinase 5 Protein 13.1 <0.01 16.8 phosphatase 1, catalytic alpha Protein<0.01* −35.4 <0.01* −63.2 <0.01* −21.4 phosphatase 1, regulatory 3CPhosphatidylinositol Signaling Pathway Inositol <0.01 13.2 <0.05 12.2polyphosphate-5- phosphatase A Inositol <0.01* 21.8 polyphosphate-5-phosphatase F Inositol 1,4,5- 14.8 <0.05 11.5 <0.01 −12.7 <0.05 −12.3<0.01* −34.0 trisphosphate 3- kinase B Inositol 21.5 <0.01* 24.9polyphosphate-1- phosphatase CDP- −29.5 diacylglycerol synthase 1Phosphoinositide- <0.05 −14.1 <0.01* −35.9 3-kinase catalytic 2APhosphoinositide- 16.6 <0.01 14.8 3-kinase catalytic 2BPhosphoinositide- −32.0 3-kinase regulatory 1 Protein kinase C −29.5iota Inositol 1,4,5- <0.05 13.0 <0.01 17.4 triphosphate receptor 1Protein kinase C <0.01 14.8 <0.01 11.5 beta 1

TABLE 15 Bipolar Disorder U95Av2 Cohort A UniGene GDB P Name Symbol IDAccession # G protein Cytoband Value % FC Protein phosphatase PPP1R3CHs.303090 BX537399 10q23-q24 1 regulatory 3C Phosphodiesterase PDE8AHs.9333 NM_173457 15q25 8A Inositol 1,4,5- ITPKB Hs.528087 AJ242780 1q42trisphosphate 3- kinase B G protein beta 5 GNB5 Hs.155090 AK092059 15q21Somatostatin SST Hs.12409 BI918626 Gi 3q28 <0.01 −16.8 Adrenergic,beta-1-, ADRB1 Hs.99913 BC045633 Gs 10q24-q26 <0.01 −18.4 receptorGlutamate receptor, GRM3 Hs.112621 BC041407 Gi 7q21 <0.01* 28.4metabotropic 3 G protein-coupled GPRC5B Hs.148685 NM_016235 Unknown16p12 <0.01* 31.8 receptor C-5-B G protein-coupled GPR37 Hs.406094BX649006 Unknown 7q31 receptor 37 G protein-coupled GPR56 Hs.513633NM_201524 Unknown 16q13 receptor 56 Bipolar Disorder Major DepresiveDisorder U133A U95Av2 U133A U133A Cohort A Cohort A Cohort A Cohort B PP P P Name Value % FC Value % FC Value % FC Value % FC Proteinphosphatase <0.01* −26.4 <0.01* −62.5 <0.01* −29.6 1 regulatory 3CPhosphodiesterase <0.01* −32.0 8A Inositol 1,4,5- <0.01 −12.5 <0.01*−46.1 trisphosphate 3- kinase B G protein beta 5 <0.05 12.8 <0.01 18.7Somatostatin <0.01* −25.7 <0.01* −26.6 <0.01* −34.2 Adrenergic, beta-1-,<0.05 −13.4 receptor Glutamate receptor, metabotropic 3 Gprotein-coupled <0.01* −35.6 <0.01* −34.3 <0.01* −24.0 receptor C-5-B Gprotein-coupled <0.01* −62.5 receptor 37 G protein-coupled <0.01 −14.2<0.01* −20.0 <0.01* −23.2 receptor 56

TABLE 16 BPD MDD U95Av2 U95Av2 Name Symbol UniGene ID GDB Accession # Gprotein Cytoband P Value % FC P Value % FC Phosphodiesterase 4B PDE4BHs.198072 CR749667 1p31 <0.01* −45.3 Inositol polyphosphate-5- INPP5AHs.523360 NM_005539 10q26 <0.01* 26.1 phosphatase A Regulator ofG-protein RGS20 Hs.368733 AK094559 8q12 <0.01* −23.8 signalling 20Proenkephalin PENK Hs.339831 AK091563 Gi 8q23-q24 <0.01* 83.4 <0.01*34.5 G protein-coupled receptor GPRC5B Hs.148685 NM_016235 Unknown 16p12<0.01* −31.7 C-5-B G protein-coupled receptor GPR37 Hs.406094 BX649006Unknown 7q31 <0.01* −42.4 37

TABLE 17 BPD vs Control MDD vs Control UniGene Gene Name Symbol U95Av2 %FC U133A % FC qRT-PCR % FC U95Av2 % FC U133A % FC qRT-PCR % FC Hs.1832Neuropeptide NPY 22.1 ** 33.0 ** 37.6 * Y Hs.12409 Somatostatin SST 29.0** 22.1 ** N.S. Hs.148685 G protein- GPRC5B 38.4 ** 24.6 ** 46.8 * −36.5** −38.3 ** −54.0 ** coupled receptor C-5-B Hs.406094 G protein- GPR3753.1 ** 38.3 ** 54.1 * −53.5 ** −40.5 ** −62.7 * coupled receptor 37Hs.368733 Regulator of RGS20 −28.2 ** −29.2 ** −36.9 ** G-proteinsignalling 20 Hs.303090 Protein PPP1R3C −35.4 ** −63.2 ** −46.1 **phosphatase 1 regulatory subunit 3C Hs.32309 Inositol INPP1 21.5 ** 24.9** 21.7 * polyphosphate- 1-phosphatase

TABLE 18 BP - Control UniGene Amy 133A-22 HC 133A-22 nAcc 133A-22 NameSymbol ID UGRepAcc Cytoband p-value % FC p-value % FC p-value % FCLigands Adrenomedullin ADM Hs.441047 CR603703 11p15 <0.01* 31.53Brain-specific angiogenesis BAI3 Hs.13261 AB011122 6q12 <0.01* 22.18<0.01* 36.44 inhibitor 3 Cholecystokinin CCK Hs.458426 BC028133 3p22-p21<0.01* 58.95 <0.01* 75.64 Somatostatin SST Hs.12409 BI918626 3q28 <0.01*43.64 Chemokine (C—C motif) CCL25 Hs.310511 CR603063 19p13 <0.01* −23.50ligand 25 Chemokine (C—X—C motif) CXCL14 Hs.483444 NM_004887 5q31 <0.01*−21.63 <0.01* −37.40 <0.01* −26.52 ligand 14 Frizzled homolog 7(Drosophila) FZD7 Hs.173859 AB017365 2q33 <0.01* 26.17 Monoamine oxidaseB MAOB Hs.46732 NM_000898 Xp113 <0.01* 21.95 Neuropeptide Y NPY Hs.1832BF680552 7p15 <0.01* 27.35 Neurotensin NTS Hs.80962 BF698911 12q21<0.01* 31.10 Prodynorphin PDYN Hs.22584 BC026334 20pter-p12 <0.01* 73.04<0.01* 20.40 Proenkephalin PENK Hs.339831 AK091563 8q23-q24 <0.01*121.58 <0.01 19.08 GPCR Neuropeptide Y receptor Y1 NPY1R Hs.519057L07615 4q31-q32 <0.01* 42.45 Gamma-aminobutyric acid GABRD Hs.113882NM_000815 1p <0.01* 27.99 (GABA) A receptor, delta Neurotensin receptor2 NTSR2 Hs.131138 NM_012344 2p25 <0.01* −26.66 Oxytocin receptor OXTRHs.2820 NM_000916 3p25 <0.01* −27.98 Adenosine A2a receptor ADORA2AHs.197029 BC013780 22q11 <0.01* 42.45 Cadherin, EGF LAG seven-passCELSR2 Hs.57652 AF234887 1p21 <0.01* 20.09 G-type receptor 2 Gprotein-coupled receptor 116 GPR116 Hs.362806 BC066121 6p12 <0.01*−33.15 G protein-coupled receptor 125 GPR125 Hs.99195 XM_291111 4p15<0.05 −11.08 G protein-coupled receptor 17 GPR17 Hs.46453 AK126849 2q21<0.05 8.77 G protein-coupled receptor 22 GPR22 Hs.432557 AK1226217q22-q31 <0.05 12.47 G protein-coupled receptor 37 GPR37 Hs.406094BX649006 7q31 <0.01 −16.70 G protein-coupled receptor 51 GPR51 Hs.198612AF056085 9q22-q22 <0.01 −19.60 <0.01 15.51 <0.01* 23.38 Gprotein-coupled receptor 6 GPR6 Hs.46332 NM_005284 6q21 <0.01* 78.20<0.01* 24.14 G protein-coupled receptor, GPRC5B Hs.148685 NM_01623516p12 <0.01 11.08 C-5-B Glutamate receptor, GRM3 Hs.112621 BC041407 7q21<0.01* 28.68 metabotropic 3 Histamine receptor H3 HRH3 Hs.251399NM_007232 20q13 <0.01 18.90 Dopamine receptor D1 DRD1 Hs.2624 NM_0007945q35 <0.01* 53.37 <0.05 17.68 Endothelin receptor type B EDNRB Hs.82002NM_000115 13q22 <0.01* 24.03 <0.01* −37.40 5-hydroxytryptamine(serotonin) HTR2C Hs.149037 NM_000868 Xq24 <0.01* 97.85 <0.01* 24.17<0.01* 33.87 receptor 2C G protein G protein, alpha inhibiting GNAI1Hs.134587 BC026326 7q21 <0.01* 22.98 <0.01* 32.60 activity polypeptide 1Guanine nucleotide binding GNB1 Hs.430425 AK123609 1p36 <0.01 19.19protein, beta polypeptide 1 Guanine nucleotide binding GNB5 Hs.155090AK092059 15q21 <0.01 19.68 <0.01* 21.92 protein (G protein), beta 5Guanine nucleotide binding GNG3 Hs.179915 BM668891 11p11 <0.05 9.70<0.01* 28.84 <0.01* 31.30 protein (G protein), gamma 3 Guaninenucleotide binding GNG7 Hs.515544 AK024465 19p13 <0.01* 25.24 protein (Gprotein), gamma 7 Regulator of G protein signaling Regulator ofG-protein RGS1 Hs.75256 AK093544 1q31 <0.05 −9.16 signalling 1 Regulatorof G-protein RGS2 Hs.78944 BC042755 1q31 <0.01* 23.56 <0.01* 20.60signalling 2 Regulator of G-protein RGS20 Hs.368733 AK094559 8q12 <0.01*25.58 signalling 20 Regulator of G-protein RGS4 Hs.386726 NM_005613 1q23<0.05 −8.25 <0.01* 21.82 signalling 4 Regulator of G-protein RGS5Hs.24950 NM_003617 1q23 <0.01* −26.85 <0.01* −32.51 <0.01* −20.65signalling 5 Regulator of G-protein RGS7 Hs.130171 CR627366 1q43 <0.0118.39 signalling 7 Regulator of G-protein RGS9 Hs.132327 BC02250417q23-q24 <0.01* 25.58 signalling 9 Cyclic AMP signaling Protein kinase,PRKACB Hs.487325 BX537705 1p36 <0.01* 26.80 <0.01* 20.88 <0.01* 22.95cAMP-dependent, catalytic, beta Protein kinase, PRKAR1A Hs.280342CR749311 17q23-q24 <0.01* 21.71 <0.01* 23.64 <0.01* 26.15cAMP-dependent, regulatory, type I, alpha Protein kinase, PRKAR2BHs.433068 BC075800 7q22 <0.01* 23.30 <0.01* 54.89 cAMP-dependent,regulatory, type II, beta Protein kinase PKIA Hs.433700 NM_006823 8q21<0.01* 30.00 (cAMP-dependent, catalytic) inhibitor alphaPhosphodiesterase 8A PDE8A Hs.9333 NM_173457 15q25 <0.01* −25.56 CyclicAMP ARPP-19 Hs.512908 AL833077 15q21 <0.01* 27.29 <0.01 19.35phosphoprotein, 19 kD Adenylate cyclase-associated CAP2 Hs.132902NM_006366 6p22 <0.05 10.52 <0.01* 35.43 protein, 2 Cyclin-dependentkinase 5 CDK5 Hs.166071 AK026533 7q36 <0.01* 20.85 Phosphatidylinositolsignaling Diacylglycerol kinase, DGKB Hs.487619 NM_004080 7p21 <0.0118.61 <0.01* 26.46 beta 90 kDa Inositol polyphosphate-5- INPP5AHs.523360 NM_005539 10q26 <0.01* 34.39 <0.01* 27.86 phosphatase Inositolpolyphosphate-5- INPP5F Hs.369755 NM_014937 10q26 <0.01* 31.06 <0.01*29.81 phosphatase F Inositol 1,4,5-triphosphate ITPR1 Hs.374613 D260703p26-p25 <0.01* 23.50 <0.01* 29.24 receptor, type 1Phosphatidylinositol-4- PIP5K1B Hs.534371 BC030587 9q13 <0.01* 20.75phosphate 5-kinase, type I, beta Phosphatidylinositol-4- PIP5K2CHs.144502 AK125526 12q13 <0.01* 23.03 phosphate 5-kinase, type II, gammaPhospholipase C, beta 1 PLCB1 Hs.310537 NM_182734 20p12 <0.01 19.28(phosphoinositide- specific) Protein kinase C, beta 1 PRKCB1 Hs.460355AL833252 16p11 <0.01* 23.66 <0.01 18.25 Myristoylated alanine-richMARCKS Hs.519909 NM_002356 6q22 <0.01* 23.12 protein kinase C substrateGrowth associated protein 43 GAP43 Hs.134974 AK091466 3q13 <0.01* 27.99<0.01* 46.79 YWHA Tyrosine 3-monooxygenase/ YWHAB Hs.279920 NM_00340420q13 <0.01* 37.20 <0.01* 22.45 tryptophan 5-monooxygenase activationprotein, beta polypeptide Chromosome 22 open reading YWHAH Hs.226755CR622695 22q12 <0.01* 73.39 <0.01* 66.65 frame 24 Tyrosine3-monooxygenase/ YWHAQ Hs.74405 NM_006826 2p25 <0.01* 32.96 tryptophan5-monooxygenase activation protein, theta polypeptide Tyrosine3-monooxygenase/ YWHAZ Hs.492407 BC051814 8q23 <0.01 13.55 <0.01* 42.25<0.01* 31.83 tryptophan 5-monooxygenase activation protein, zetapolypeptide Calcium signaling Calmodulin 1 (phosphorylase CALM1Hs.282410 BC047523 14q24-q31 <0.01* 21.80 kinase, delta) Calmodulin 3(phosphorylase CALM3 Hs.515487 AK094964 19q13 <0.01* 30.65 kinase,delta) Calcium/calmodulin-dependent CAMK1 Hs.434875 AK094026 3p25 <0.0518.27 protein kinase I Calcium/calmodulin-dependent CAMK2A Hs.143535NM_015981 5q32 <0.01* 20.41 protein kinase II alphaCalcium/calmodulin-dependent CAMK2B Hs.351887 NM_001220 22q12 <0.01*21.93 protein kinase II beta Calmodulin binding transcription CAMTA1Hs.397705 NM_015215 1p36 <0.01 16.05 <0.05 14.94 activator 1Doublecortin and CaM DCAMKL1 Hs.507755 NM_004734 13q13 <0.01* 29.98kinase-like 1 MAPK signaling P21/Cdc42/Rac1-activated PAK1 Hs.435714NM_002576 11q13-q14 <0.05 13.71 <0.01 16.23 kinase 1 (STE20 homolog,yeast) Mitogen-activated protein MAP2K1 Hs.145442 NM_002755 15q22 <0.01*33.40 <0.01* 57.55 <0.01* 46.39 kinase kinase 1 Mitogen-activatedprotein MAP2K1IP1 Hs.433332 AK022313 4q23 <0.01* 20.94 kinase kinase 1interacting protein 1 Mitogen-activated protein MAP2K4 Hs.514681AK131544 17p11 <0.01 17.47 <0.01* 29.05 <0.01* 22.97 kinase kinase 4Mitogen-activated protein MAP4K4 Hs.431550 NM_145686 2q11-q12 <0.01*−23.32 kinase kinase kinase kinase 4 Mitogen-activated MAPK1 Hs.431850NM_002745 22q11 <0.01* 31.80 <0.01* 52.27 <0.01* 41.35 protein kinase 1Mitogen-activated MAPK10 Hs.25209 AK124791 4q22-q23 <0.01* 25.47 proteinkinase 10 Mitogen-activated MAPK9 Hs.484371 BC032539 5q35 <0.01 13.93<0.01* 22.88 protein kinase 9 Protein Phosphatase Protein phosphatase 1,PPP1CC Hs.79081 NM_002710 12q24 <0.01* 25.65 catalytic subunit, gammaisoform Protein phosphatase 1, PPP1R2 Hs.184840 NM_006241 3q29 <0.01*21.53 regulatory (inhibitor) subunit 2 Protein phosphatase 1, PPP1R3CHs.303090 BX537399 10q23-q24 <0.01 −16.80 <0.01* −47.55 regulatorysubunit 3C Protein phosphatase 2C, PPM2C Hs.22265 NM_018444 8q22 <0.0523.33 magnesium- dependent, catalytic subunit Protein phosphatase 2(formerly PPP2CA Hs.483408 BX640662 5q23-q31 <0.01* 24.59 2A), catalyticsubunit, alpha isoform Protein phosphatase 2 (formerly PPP2R1A Hs.467192AK090488 19q13 <0.01* 27.34 <0.01* 24.11 2A), regulatory subunit A (PR65), alpha isoform Protein phosphatase 2 (formerly PPP2R2B Hs.193825M64930 5q31-5q32 <0.01* 38.94 2A), regulatory subunit B (PR 52), betaisofrom Protein phosphatase 2, PPP2R5C Hs.368264 NM_002719 14q32 <0.01*23.54 regulatory subunit B (B56), gamma isoform Protein phosphatase 3PPP3CA Hs.435512 NM_000944 4q21-q24 <0.01* 29.94 <0.01* 23.23 (formerly2B), catalytic subunit, alpha isoform (calcineurin A alpha) Proteinphosphatase 3 PPP3CB Hs.500067 BC028049 10q21-q22 <0.01* 20.95 <0.01*45.82 <0.01* 31.17 (formerly 2B), catalytic subunit, beta isform(calcineurin A beta) Protein phosphatase 3 PPP3R1 Hs.280604 BC0279132p15 <0.01* 25.69 (formerly 2B), regulatory subunit B, 19 kDa, alphaisoform (calcineurin B, type I) AP1 V-fos FBJ murine osteosarcoma FOSHs.25647 BX647104 14q24 <0.01* −40.86 <0.01* −80.23 viral oncogenehomolog V-jun sarcoma virus 17 JUN Hs.525704 NM_002228 1p32-p31 <0.01*−25.24 oncogene homolog (avian) Small G protein Rho guanine nucleotideARHGEF3 Hs.476402 AL833224 3p21-p13 <0.01* 31.85 exchange factor (GEF) 3Ras homolog gene family, ARHI Hs.194695 AK096393 1p31 <0.01* 132.94<0.01* 33.15 member I DIRAS family, GTP-binding DIRAS2 Hs.165636NM_017594 9q22 RAS-like 2 RAB31, member RAS RAB31 Hs.99528 NM_00686818p11 <0.05 −9.44 oncogene family RAB33A, member RAB33A Hs.56294AK094927 Xq25 <0.01* 21.72 RAS oncogene family Rab acceptor 1(prenylated) RABAC1 Hs.11417 BE779053 19q13 <0.01* 21.97 RAN bindingprotein 6 RANBP6 Hs.167496 BX537405 9p24 <0.01* 25.82 RAP1, GTPaseRAP1GA1 Hs.148178 BC035030 1p36-p35 <0.01* 52.74 activating protein 1Hypothetical protein RASGRF1 Hs.459035 NM_002891 15q24 <0.01* 28.36LOC145899 RAS guanyl releasing protein 1 RASGRP1 Hs.511010 AF08119515q15 <0.01* 24.37 (calcium and DAG-regulated) RAS guanyl releasingprotein 3 RASGRP3 Hs.143674 BC027849 2p25-p24 <0.01 −14.27 (calcium andDAG-regulated) Ras-like without CAAX 2 RIT2 Hs.464985 AL713637 18q12<0.01* 32.56 RAS-related on chromosome 22 RRP22 Hs.73088 NM_00100727922q12 <0.01* 20.87 V-Ki-ras2 Kirsten rat sarcoma 2 KRAS2 Hs.505033NM_033360 12p12 <0.01* 22.38 viral oncogene homolog Ras-GTPaseactivating protein G3BP2 Hs.303676 NM_203505 4q21 <0.01* 23.35 <0.01*36.80 SH3 domain- binding protein 2 Potassium channel Potassium channelKCMF1 Hs.345694 NM_020122 2p11 <0.01* 22.07 modulatory factor 1Potassium voltage-gated KCNAB2 Hs.440497 AK124696 1p36 <0.01* 24.09channel, shaker- related beta 2 Potassium voltage-gated KCND2 Hs.21703AB028967 7q31 <0.01* 20.05 channel, Shal-related 2 Potassiuminwardly-rectifying KCNJ2 Hs.1547 NM_000891 17q23-q24 <0.01* −28.13channel, subfamily J 2 Potassium inwardly-rectifying KCNJ6 Hs.50927AK058042 21q22 <0.01* 26.12 channel, subfamily J 6 Potassiuminwardly-rectifying KCNJ13 Hs.467338 NM_002242 2q37 <0.01* 31.87channel, subfamily J 13 Potassium channel, subfamily KCNK1 Hs.208544AL833343 1q42-q43 <0.01* 23.33 K, member 1 Potassium intermediate/ KCNN2Hs.98280 NM_021614 5q22 <0.01* 28.96 small conductance calcium-activatedchannel, subfamily N, member 2 Potassium intermediate/ KCNN3 Hs.490765BX649146 1q21 <0.01 −13.90 small conductance calcium-activated channel,subfamily N, member 3 Potassium channel, KCNV1 Hs.13285 NM_0143798q22-q24 <0.01 11.16 subfamily V, member 1 Sodium channel Sodiumchannel, SCN3B Hs.4865 AB032984 11q24 <0.01* 41.71 <0.01* 37.41voltage-gated, type III, beta Solute carrier family 12, SLC12A5 Hs.21413NM_020708 20q132 <0.01 11.53 <0.01* 21.22 (potassium-chloridetransporter) member 5 Solute carrier family 24 SLC24A3 Hs.211252AL833544 20p13 <0.01* 60.32 (sodium/potassium/ calcium exchanger),member 3 Voltage-dependent VDAC1 Hs.519320 AK122953 5q31 <0.01* 27.48anion channel 1 Calcium Channel Calcium channel, CACNA2D3 Hs.369421NM_018398 3p21 <0.01* 36.34 voltage-dependent, alpha 2/delta 3 Calciumchannel, CACNB2 Hs.59093 NM_000724 10p12 <0.01* 21.04 <0.01* 23.85voltage-dependent, beta 2 subunit Calcium channel, CACNB3 Hs.250712AK122911 12q13 <0.01* 22.11 voltage-dependent, beta 3 subunit Calciumchannel, CACNG3 Hs.7235 AK095553 16p12-p13 <0.01* 32.54voltage-dependent, gamma subunit 3 Chloride channel Chlorideintracellular channel 4 CLIC4 Hs.440544 AL117424 1p36 <0.05 −17.97

TABLE 19 MD - Control UniGene Amy 133A-22 HC 133A-22 nAcc 133A-22 NameSymbol ID UGRepAcc Cytoband p-value % FC p-value % FC p-value % FCLigands Adrenomedullin ADM Hs.441047 CR603703 11p15 <0.05 −7.16 <0.01*−34.24 Brain-specific BAI3 Hs.13261 AB011122 6q12 <0.01* 20.13 <0.01*20.61 angiogenesis inhibitor 3 Cholecystokinin CCK Hs.458426 BC0281333p22-p21 <0.01* 29.74 <0.01* 81.09 Somatostatin SST Hs.12409 BI9186263q28 <0.01* 20.70 Frizzled homolog 7 FZD7 Hs.173859 AB017365 2q33 <0.058.11 (Drosophila) Latrophilin 2 LPHN2 Hs.24212 AF104266 1p31 <0.01*29.33 Prodynorphin PDYN Hs.22584 BC026334 20pter-p12 <0.01* 34.43 <0.01*31.55 Proenkephalin PENK Hs.339831 AK091563 8q23-q24 <0.01* 57.92 <0.01*21.80 <0.01* 22.13 Prostaglandin D2 synthase PTGDS Hs.446429 BM8058079q34-q34 <0.01* −23.24 21 kDa (brain) GPCR Neuropeptide Y receptor Y1NPY1R Hs.519057 L07615 4q31-q32 <0.01* 44.09 Gamma-aminobutyric GABRDHs.113882 NM_000815 1p <0.01* 22.04 <0.01* 22.85 acid (GABA) A receptor,delta Neurotensin receptor 2 NTSR2 Hs.131138 NM_012344 2p25 <0.01*−37.48 <0.01 −17.42 Oxytocin receptor OXTR Hs.2820 NM_000916 3p25 <0.01−15.90 Cholecystokinin B receptor CCKBR Hs.203 AF239668 11p15 <0.01*27.01 Adenosine A2a receptor ADORA2A Hs.197029 BC013780 22q11 <0.0118.30 <0.01* 23.23 Angiotensin II receptor-like 1 AGTRL1 Hs.438311AK075252 11q12 <0.01* −22.99 G protein-coupled receptor 125 GPR125Hs.99195 XM_291111 4p15 <0.01* −22.88 G protein-coupled receptor 17GPR17 Hs.46453 AK126849 2q21 <0.01* −27.08 G protein-coupled receptor 22GPR22 Hs.432557 AK122621 7q22-q31 <0.01* 24.51 G protein-coupledreceptor 37 GPR37 Hs.406094 BX649006 7q31 <0.01* −43.90 G-proteincoupled receptor GPR37L1 Hs.132049 BC050334 1q32 <0.01* −27.67 37 like 1G protein-coupled receptor 51 GPR51 Hs.198612 AF056085 9q22-q22 <0.01*31.80 <0.01* 29.07 G protein-coupled receptor 56 GPR56 Hs.513633NM_201524 16q13 <0.01* −24.98 G protein-coupled receptor 6 GPR6 Hs.46332NM_005284 6q21 <0.01* 27.88 <0.01* 41.21 Chemokine (C—X—C motif) CXCR4Hs.421986 CR614663 2q21 <0.01* −20.68 receptor 4 G protein-coupledGPRC5B Hs.148685 NM_016235 16p12 <0.01* −27.94 <0.01* −36.01 receptor,C-5-B Histamine receptor H3 HRH3 Hs.251399 NM_007232 20q13 <0.01* 30.42Dopamine receptor D1 DRD1 Hs.2624 NM_000794 5q35 <0.01* 27.79 <0.01*25.88 Endothelial differentiation, EDG1 Hs.154210 BC018650 1p21 <0.01*−20.04 sphingolipid GPCR 1 Endothelin receptor EDNRB Hs.82002 NM_00011513q22 <0.01* −64.83 <0.01 −14.45 <0.01* −37.17 type B5-hydroxytryptamine HTR2A Hs.424980 NM_000621 13q14-q21 <0.01* 45.03<0.01* 42.32 (serotonin) receptor 2A 5-hydroxytryptamine HTR2C Hs.149037NM_000868 Xq24 <0.01 14.27 <0.01 −18.49 <0.01* 31.98 (serotonin)receptor 2C G protein Guanine nucleotide GNA13 Hs.515018 NM_006572 17q24<0.01* −20.84 binding protein (G protein), alpha 13 G protein, alphaGNAI1 Hs.134587 BC026326 7q21 <0.05 17.13 inhibiting activitypolypeptide 1 Guanine nucleotide GNB1 Hs.430425 AK123609 1p36 <0.01*22.06 binding protein, beta polypeptide 1 Guanine nucleotide GNB5Hs.155090 AK092059 15q21 <0.01* 24.99 <0.01* 32.65 binding protein (Gprotein), beta 5 Guanine nucleotide GNG12 Hs.431101 NM_018841 1p31<0.01* −21.46 binding protein (G protein), gamma 12 Guanine nucleotideGNG3 Hs.179915 BM668891 11p11 <0.01* 26.57 <0.01* 41.14 <0.05 14.55binding protein (G protein), gamma 3 Regulator of G protein signalingRegulator of G-protein signalling 1 RGS1 Hs.75256 AK093544 1q31 <0.01*−34.56 Regulator of G-protein signalling 2 RGS2 Hs.78944 BC042755 1q31<0.01* 36.07 <0.01 17.15 Regulator of G-protein RGS20 Hs.368733 AK0945598q12 <0.01* −32.34 signalling 20 Regulator of G-protein signalling 4RGS4 Hs.386726 NM_005613 1q23 <0.01* 72.22 <0.01* 40.31 <0.05 10.50Regulator of G-protein signalling 5 RGS5 Hs.24950 NM_003617 1q23 <0.018.03 Regulator of G-protein signalling 7 RGS7 Hs.130171 CR627366 1q43<0.01* 36.06 <0.01* 36.42 Regulator of G-protein signalling 9 RGS9Hs.132327 BC022504 17q23-q24 <0.01 11.68 Cyclic AMP signaling Proteinkinase, cAMP- PRKACB Hs.487325 BX537705 1p36 <0.01 17.60 <0.01 16.51dependent, catalytic, beta Protein kinase, PRKAR1A Hs.280342 CR74931117q23-q24 <0.01 11.92 <0.05 10.27 cAMP-dependent, regulatory, type I,alpha (tissue specific extinguisher 1) Protein kinase, PRKAR2B Hs.433068BC075800 7q22 <0.01* 26.41 <0.01* 52.17 cAMP-dependent, regulatory, typeII, beta Protein kinase (cAMP- PKIA Hs.433700 NM_006823 8q21 <0.05 14.78dependent, catalytic) inhibitor alpha Phosphodiesterase PDE4DIPHs.487925 NM_014644 1q12 <0.01* −21.98 4D interacting protein(myomegalin) Phosphodiesterase 8A PDE8A Hs.9333 NM_173457 15q25 <0.01*−20.78 <0.01* −39.39 Phosphodiesterase 8B PDE8B Hs.78106 AF079529 5q13<0.01* 20.36 Cyclic AMP phosphoprotein, ARPP-19 Hs.512908 AL833077 15q21<0.01* 24.18 <0.01* 25.33 <0.01* 27.45 19 kD Adenylate cyclase- CAP2Hs.132902 NM_006366 6p22 <0.01* 32.38 <0.01* 27.21 associated protein, 2Cyclin-dependent CDK5 Hs.166071 AK026533 7q36 <0.01 18.67 kinase 5Phosphatidylinositol signaling Diacylglycerol kinase, DGKB Hs.487619NM_004080 7p21 <0.01* 32.70 <0.01* 26.36 beta 90 kDa Inositolpolyphosphate- INPP5A Hs.523360 NM_005539 10q26 <0.01* 22.52 <0.01*40.16 <0.01* 22.98 5-phosphatase, 40 kDa Inositol polyphosphate- INPP5FHs.369755 NM_014937 10q26 <0.01* 40.58 <0.01* 45.18 <0.01* 32.425-phosphatase F Inositol 1,4,5-trisphosphate ITPKA Hs.2722 BC02633115q14-q21 <0.01* 29.49 <0.01* 32.18 3-kinase A Inositol1,4,5-trisphosphate ITPKB Hs.528087 AJ242780 1q423 <0.01* −34.51 <0.01*−34.14 3-kinase B Inositol 1,4,5-triphosphate ITPR1 Hs.374613 D260703p26-p25 <0.01* 45.62 <0.01* 51.25 receptor, type 1Phosphoinositide-3-kinase, PIK3C2A Hs.175343 BX648778 11p15-p14 <0.01*−63.06 class 2, alpha polypeptide Phosphoinositide-3-kinase, PIK3C2AHs.175343 BX648778 11p15-p14 <0.01* −63.06 class 2, alpha polypeptidePhosphatidylinositol-4- PIP5K1B Hs.534371 BC030587 9q13 <0.01* 24.44phosphate 5-kinase, type I, beta Phosphatidylinositol-4- PIP5K2CHs.144502 AK125526 12q13 <0.05 17.13 phosphate 5-kinase, type II, gammaPhospholipase C, beta PLCB1 Hs.310537 NM_182734 20p12 <0.01* 26.19 1(phosphoinositide- specific) Protein kinase C, beta 1 PRKCB1 Hs.460355AL833252 16p11 <0.01* 51.20 <0.01* 43.94 Growth associated GAP43Hs.134974 AK091466 3q13 <0.01* 49.55 <0.01* 30.12 protein 43 YWHATyrosine 3-monooxygenase/ YWHAB Hs.279920 NM_003404 20q13 <0.01* 20.42<0.01* 30.24 <0.05 13.58 tryptophan 5- monooxygenase activation protein,beta polypeptide Chromosome 22 open YWHAH Hs.226755 CR622695 22q12<0.01* 31.18 <0.01* 56.74 <0.01* 26.27 reading frame 24 Tyrosine3-monooxygenase/ YWHAZ Hs.492407 BC051814 8q23 <0.01* 20.06 <0.01* 30.03<0.01* 20.91 tryptophan 5- monooxygenase activation protein, zetapolypeptide Calcium signaling Calmodulin 1 (phosphorylase CALM1Hs.282410 BC047523 14q24-q31 <0.01 16.48 kinase, delta) Calmodulin 3(phosphorylase CALM3 Hs.515487 AK094964 19q13 <0.01 14.08 kinase, delta)Calcium/calmodulin- CAMK1 Hs.434875 AK094026 3p25 <0.01* 20.75 dependentprotein kinase I Calcium/calmodulin- CAMK2A Hs.143535 NM_015981 5q32<0.01* 30.59 dependent protein kinase II alpha Calcium/calmodulin-CAMK2B Hs.351887 NM_001220 22q12 <0.05 13.91 dependent protein kinase IIbeta Calcium/calmodulin- CaMKIINalpha Hs.197922 CR604926 1p36 <0.01*21.16 dependent protein kinase II Calcium/calmodulin- CAMKK2 Hs.297343NM_006549 12q24 <0.01* 22.16 dependent protein kinase kinase 2, betaCalmodulin binding CAMTA1 Hs.397705 NM_015215 1p36 <0.01* 31.29 <0.01*41.27 transcription activator 1 Doublecortin and CaM DCAMKL1 Hs.507755NM_004734 13q13 <0.05 16.77 kinase-like 1 MAPK signaling P21/Cdc42/Rac1-PAK1 Hs.435714 NM_002576 11q13-q14 <0.01* 32.71 <0.01* 36.58 activatedkinase 1 (STE20 homolog, yeast) Mitogen-activated MAP2K1 Hs.145442NM_002755 15q22 <0.01* 23.61 <0.01* 35.94 <0.01* 26.19 protein kinasekinase 1 Mitogen-activated MAP2K1IP1 Hs.433332 AK022313 4q23 <0.05 13.15protein kinase kinase 1 interacting protein 1 Mitogen-activated MAP2K4Hs.514681 AK131544 17p11 <0.01* 23.15 <0.01 19.77 <0.05 8.77 proteinkinase kinase 4 Mitogen-activated MAP4K4 Hs.431550 NM_145686 2q11-q12<0.01* −24.08 protein kinase kinase kinase kinase 4 Mitogen-activatedMAP4K5 Hs.130491 NM_198794 14q11-q21 <0.01* −24.23 protein kinase kinasekinase kinase 5 Mitogen-activated MAPK1 Hs.431850 NM_002745 22q11 <0.059.57 <0.01* 22.13 protein kinase 1 Mitogen-activated MAPK10 Hs.25209AK124791 4q22-q23 <0.01* 21.09 protein kinase 10 Mitogen-activated MAPK6Hs.411847 NM_002748 15q21 <0.01* 23.03 protein kinase 6Mitogen-activated MAPK9 Hs.484371 BC032539 5q35 <0.01* 21.30 <0.05 12.07protein kinase 9 Protein Phosphatase Protein phosphatase PPP1R2Hs.184840 NM_006241 3q29 <0.01* 20.02 1, regulatory (inhibitor) subunit2 Protein phosphatase PPP1R3C Hs.303090 BX537399 10q23-q24 <0.01* −54.15<0.01* −47.47 <0.01* −43.72 1, regulatory subunit 3C Protein phosphatase2C, PPM2C Hs.22265 NM_018444 8q22 <0.01* 35.09 <0.01* 47.45 magnesium-dependent, catalytic subunit Protein phosphatase PPP2CA Hs.483408BX640662 5q23-q31 <0.01 17.92 2 (formerly 2A), catalytic subunit, alphaisoform Protein phosphatase 2 PPP2R1A Hs.467192 AK090488 19q13 <0.0516.04 <0.05 12.64 (formerly 2A), regulatory subunit A (PR 65), alphaisoform Protein phosphatase PPP2R2B Hs.193825 M64930 5q31-5q32 <0.01*29.87 2 (formerly 2A), regulatory subunit B (PR 52), beta isoformProtein phosphatase 2, PPP2R5C Hs.368264 NM_002719 14q32 <0.01 18.07regulatory subunit B (B56), gamma isoform Protein phosphatase PPP3CAHs.435512 NM_000944 4q21-q24 <0.01* 43.20 <0.01* 26.06 3 (formerly 2B),catalytic subunit, alpha isoform (calcineurin A alpha) Proteinphosphatase PPP3CB Hs.500067 BC028049 10q21-q22 <0.01* 37.18 <0.01*47.07 <0.01 17.08 3 (formerly 2B), catalytic subunit, beta isoform(calcineurin A beta) Protein phosphatase PPP3R1 Hs.280604 BC027913 2p15<0.01* 33.47 <0.01* 31.25 3 (formerly 2B), regulatory subunit B, 19 kDa,alpha isoform (calcineurin B, type I) AP1 V-fos FBJ murine FOS Hs.25647BX647104 14q24 <0.01* −55.69 <0.01* −46.49 osteosarcoma viral oncogenehomolog Small G protein Rho guanine nucleotide ARHGEF3 Hs.476402AL833224 3p21-p13 <0.01* 28.51 exchange factor (GEF) 3 Ras homolog geneARHI Hs.194695 AK096393 1p31 <0.05 20.60 <0.01* 28.06 family, member IDIRAS family, DIRAS2 Hs.165636 NM_017594 9q22 <0.01* 63.78 GTP-bindingRAS-like 2 RAB31, member RAS RAB31 Hs.99528 NM_006868 18p11 <0.01*−27.47 oncogene family Rab acceptor 1 (prenylated) RABAC1 Hs.11417BE779053 19q13 <0.01 16.11 RAN binding protein 6 RANBP6 Hs.167496BX537405 9p24 <0.05 17.28 RAP1, GTPase RAP1GA1 Hs.148178 BC0350301p36-p35 <0.01* 22.75 activating protein 1 Hypothetical protein RASGRF1Hs.459035 NM_002891 15q24 <0.01* 26.84 LOC145899 RAS guanyl releasingRASGRP1 Hs.511010 AF081195 15q15 <0.05 18.52 protein 1 (calcium andDAG-regulated) RAS guanyl releasing RASGRP3 Hs.143674 BC027849 2p25-p24<0.01* −20.95 protein 3 (calcium and DAG-regulated) Rho-related BTBRHOBTB3 Hs.445030 NM_014899 5q15 <0.01* −24.67 domain containing 3 Rasand Rab interactor 2 RIN2 Hs.472270 NM_018993 <0.01* −37.60 Ras-likewithout CAAX 2 RIT2 Hs.464985 AL713637 18q12 <0.01* 29.34 Rho familyGTPase 1 RND1 Hs.124940 AK124288 12q12-q13 <0.01* 28.02 V-Ki-ras2Kirsten KRAS2 Hs.505033 NM_033360 12p12 <0.01* 20.01 rat sarcoma 2 viraloncogene homolog Ras-GTPase activating G3BP2 Hs.303676 NM_203505 4q21<0.01* 25.13 <0.05 17.74 protein SH3 domain-binding protein 2 Potassiumchannel Potassium channel KCMF1 Hs.345694 NM_020122 2p11 <0.01* 23.55modulatory factor 1 Potassium voltage- KCNAB2 Hs.440497 AK124696 1p36<0.05 19.97 gated channel, shaker- related beta 2 Potassium inwardly-KCNJ2 Hs.1547 NM_000891 17q23-q24 <0.01* −41.14 rectifying channel,subfamily J 2 Potassium inwardly- KCNJ10 Hs.408960 NM_002241 1q22-q23<0.01* −25.25 rectifying channel, subfamily J 10 Potassium channel,KCNK1 Hs.208544 AL833343 1q42-q43 <0.05 11.05 subfamily K, member 1Potassium intermediate/ KCNN3 Hs.490765 BX649146 1q21 <0.01* −30.93<0.01* −23.10 small conductance calcium-activated channel, subfamily N,member 3 Potassium channel, KCNV1 Hs.13285 NM_014379 8q22-q24 <0.01*21.10 subfamily V, member 1 Sodium channel Sodium channel, SCN2A2Hs.470470 NM_021007 2q23-q24 <0.01* 26.22 voltage-gated, type II, alpha2 Sodium channel, SCN3B Hs.4865 AB032984 11q24 <0.01* 22.62 <0.01 17.61voltage-gated, type III, beta Solute carrier family SLC12A5 Hs.21413NM_020708 20q132 <0.01* 26.35 <0.01* 23.76 12, (potassium- chloridetransporter) member 5 Voltage-dependent VDAC1 Hs.519320 AK122953 5q31<0.01 18.44 anion channel 1 Calcium Channel Calcium channel, CACNA2D3Hs.369421 NM_018398 3p21 <0.01* 31.61 voltage-dependent, alpha 2/delta 3Calcium channel, CACNB2 Hs.59093 NM_000724 10p12 <0.01* 32.21voltage-dependent, beta 2 subunit Calcium channel, CACNB3 Hs.250712AK122911 12q13 <0.01* 43.88 voltage-dependent, beta 3 subunit Calciumchannel, CACNG3 Hs.7235 AK095553 16p12-p13 <0.01* 32.10voltage-dependent, gamma subunit 3 Chloride channel Chlorideintracellular CLIC4 Hs.440544 AL117424 1p36 <0.01* −34.30 channel 4

TABLE 20 Dorsalateral Anterior Cingulate Cortex Prefrontal CortexChromosomal Unigene FC FC FC T FC FC FC T Gene Symbol Accession GeneName Location clusters Pathway BPD MDD Control T BPD T MDD Control BPDMDD Control T BPD T MDD Control HSPA2 NM_021979 heat shock 70 kDa14q24.1 Hs.432648 Chaperone 1.36 0.68 0.69 9.00 −11.58 −12.22 1.21 0.691.01 5.95 −12.25 0.36 protein 2 SPP1 NM_000582 secreted 4q21-q25 Hs.313Apoptosis 1.28 0.84 0.36 7.67 −5.88 −35.42 1.32 0.86 0.70 8.49 −5.10−12.35 phosphoprotein 1 (osteopontin, bone sialoprotein I, earlyT-lymphocyte activation 1) TM4SF10 NM_031442 transmembrane 4 Xp11.4Hs.8769 Apoptosis 1.27 0.86 0.75 7.34 −4.73 −10.03 1.48 0.92 0.69 10.52−2.30 −10.96 superfamily member 10 CAT NM_001752 catalase 11p13Hs.395771 Oxidative 1.22 0.89 0.68 6.28 −3.94 −13.28 1.22 0.85 0.78 6.14−4.94 −8.30 Stress S100B NM_006272 S100 calcium 21q22.3 Hs.422181Apoptosis 1.21 0.94 0.68 6.39 −2.25 −14.39 1.19 0.89 0.75 5.16 −3.57−9.70 binding protein, beta (neural) NR4A1 NM_173157 nuclear receptor12q13 Hs.1119 Mitochondria 0.83 0.86 1.17 −9.63 −8.30 9.19 0.83 0.901.15 8.36 −5.21 7.06 subfamily 4, group A, member 1 BZRAP1 NM_004758benzodiazapine 17q22-q23 Hs.112499 Mitochondria 0.82 1.02 1.16 −7.050.68 6.01 1.00 0.96 1.21 0.10 −1.13 5.47 receptor (peripheral)associated protein 1 GSK3B NM_002093 glycogen synthase 3q13.3 Hs.282359Apoptosis 0.76 1.03 1.20 −9.16 0.94 7.11 0.93 1.00 1.05 −2.43 0.02 1.76kinase 3 beta COX7A1 NM_001864 cytochrome c 19q13.1 Hs.421621Mitochondria 0.73 1.15 1.36 −7.65 3.54 8.57 0.94 1.08 1.16 −1.73 2.084.48 oxidase subunit VIIa polypeptide 1 (muscle) UQCRB NM_006294ubiquinol- 8q22 Hs.131255 Mitochondria 1.06 1.20 0.98 1.64 5.37 −0.581.15 1.09 1.14 3.48 2.16 3.62 cytochrome c reductase binding proteinDUSP1 NM_004417 dual specificity 5q34 Hs.171695 Oxidative 0.87 0.74 1.10−4.00 −8.85 2.92 0.84 0.83 1.13 −4.06 −4.54 3.31 phosphatase 1 StressDUSP6 NM_001946 dual specificity 12q22-q23 Hs.298654 Apoptosis 0.84 0.701.59 −4.15 −8.89 12.26 0.96 0.77 1.77 −0.93 −5.46 13.19 phosphatase 6TM4SF10 NM_031442 transmembrane 4 Xp11.4 Hs.8769 Apoptosis 1.27 0.860.75 7.34 −4.73 −10.03 1.48 0.92 0.69 10.52 −2.30 −10.96 superfamilymember 10 ATP6V0E NM_003945 ATPase, H+ 5q35.2 Hs.440165 Lysosyme 1.150.88 0.59 2.89 −2.87 −12.33 1.36 0.90 0.63 6.10 −2.23 −10.14transporting, lysosomal 9 kDa, V0 subunit e GLUL S70290glutamate-ammonia 1q31 Hs.442669 Mitochondria 1.00 0.67 0.78 −0.07 −7.65−5.22 1.33 0.78 0.70 4.96 −4.42 −7.06 ligase (glutamine synthase) SPP1NM_000582 secreted 4q21-q25 Hs.313 Apoptosis 1.28 0.84 0.36 7.67 −5.88−35.42 1.32 0.86 0.70 8.49 −5.10 −12.35 phosphoprotein 1 (osteopontin,bone sialoprotein I, early T-lymphocyte activation 1) APG-1 NM_014278heat shock protein 4q28 Hs.135554 Chaperone 0.98 1.05 1.06 −0.22 0.640.92 1.26 1.19 0.95 2.81 2.20 −0.77 (hsp110 family) HSPA5 NM_005347 heatshock 70 kDa 9q33-q34.1 Hs.310769 Chaperone 1.07 0.98 0.94 1.78 −0.42−1.76 1.25 1.19 1.00 5.09 4.08 0.09 protein 5 (glucose- regulatedprotein, 78 kDa) GATM NM_001482 glycine 15q15.1 Hs.75335 Mitochondria1.08 0.80 0.61 2.62 −7.64 −18.24 1.23 0.78 0.79 7.34 −8.90 −9.41amidinotransferase (L-arginine:glycine amidinotransferase) CAT NM_001752catalase 11p13 Hs.395771 Oxidative 1.22 0.89 0.68 6.28 −3.94 −13.28 1.220.85 0.78 6.14 −4.94 −8.30 Stress HADHB NM_000183 hydroxyacyl- 2p23Hs.269878 Mitochondria 1.11 0.88 0.71 3.71 −5.10 −14.11 1.22 0.87 0.746.30 −4.74 −10.47 Coenzyme A dehydrogenase/3- ketoacyl-Coenzyme Athiolase/enoyl- Coenzyme A hydratase (trifunctional protein), betasubunit CCT3 NM_005998 chaperonin 1q23 Hs.1708 Chaperone 1.15 1.07 0.964.98 2.43 −1.67 1.22 1.04 1.03 5.97 1.34 0.96 containing TCP1, subunit 3(gamma) DAD1 NM_001344 defender against 14q11-q12 Hs.82890 Apoptosis1.13 1.00 0.88 4.36 0.15 −5.31 1.21 1.00 0.93 6.31 0.05 −2.86 cell death1 HSPA2 NM_021979 heat shock 70 kDa 14q24.1 Hs.432648 Chaperone 1.360.68 0.69 9.00 −11.58 −12.22 1.21 0.69 1.01 5.95 −12.25 0.36 protein 2NR4A1 NM_173157 nuclear receptor 12q13 Hs.1119 Mitochondria 0.83 0.861.17 −9.63 −8.30 9.19 0.83 0.90 1.15 −8.36 −5.21 7.06 subfamily 4, groupA, member 1 NAPG NM_003826 N-ethylmaleimide- 18p11.21 Hs.370431Mitochondria 0.94 1.07 1.69 −1.32 1.53 12.83 0.83 1.04 1.83 −3.06 0.6010.97 sensitive factor attachment protein, gamma MAPK1 NM_002745mitogen-activated 22q11.21 Hs.324473 Mitochondria 0.85 0.99 1.12 −4.35−0.35 3.34 0.82 0.96 1.07 −4.77 −1.10 1.82 protein kinase 1 DAD1NM_001344 defender against 14q11-q12 Hs.82890 Apoptosis 1.04 1.04 1.390.94 0.91 8.60 0.79 1.07 1.46 −3.99 1.14 7.17 cell death 1 STIP1NM_006819 stress-induced- 11q13 Hs.257827 Chaperone 1.17 1.16 0.97 4.504.51 −0.86 1.06 1.23 1.00 1.49 5.06 0.06 phosphoprotein 1 (Hsp70/Hsp90-organizing protein) DUSP1 NM_004417 dual specificity 5q34 Hs.171695Oxidative 0.87 0.74 1.10 −4.00 −8.85 2.92 0.84 0.83 1.13 −4.06 −4.543.31 phosphatase 1 Stress SLC25A13 NM_014251 solute carrier family7q21.3 Hs.9599 Mitochondria 1.06 0.91 0.97 2.33 −3.94 −1.55 1.03 0.831.03 1.11 −6.61 1.10 25, member 13 (citrin) PER2 NM_022817 periodhomolog 2 2q37.3 Hs.410692 Cycling 0.90 0.83 1.31 −3.22 −5.79 8.81 0.970.80 1.35 −0.76 −5.58 8.02 (Drosophila) SST NM_001048 somatostatin 3q28Hs.12409 Apoptosis 1.16 0.88 3.34 3.92 −3.70 36.03 0.85 0.78 3.71 4.96−7.89 45.04 DUSP6 NM_001946 dual specificity 12q22-q23 Hs.298654Apoptosis 0.84 0.70 1.59 −4.15 −8.89 12.26 0.96 0.77 1.77 −0.93 −5.4613.19 phosphatase 6 USP9Y NM_004654 ubiquitin specific Yq11.2 Hs.37125526S 1.05 0.85 1.91 0.89 −3.32 13.69 1.17 0.75 2.20 2.39 −4.51 13.38protease 9, Y-linked proteasome (fat facets-like, Drosophila) HSPA2NM_021979 heat shock 70 kDa 14q24.1 Hs.432648 Chaperone 1.36 0.68 0.699.00 −11.58 −12.22 1.21 0.69 1.01 5.95 −12.25 0.36 protein 2 SEMA6ANM_020796 sema domain, 5q23.1 Hs.443012 Apoptosis 0.84 0.74 0.68 −4.41−8.25 −11.00 0.92 0.62 1.10 −1.70 −10.66 2.29 transmembrane domain (TM),and cytoplasmic domain, (semaphorin) 6A

TABLE 21 QPCR QPCR Microarray fold Microarray fold fold change changefold change change Brain (BPD v (BPD (MDD v (MDD v Accession Symbol NameCytoband Region Control) v Control) Control) Control) NM_001001935ATP5A1 ATP synthase, 18q12-q21 DLPFC 1.203 1.587* 1.149 1.135 H+transporting, mitochondrial F1 complex, alpha subunit, isoform 1,cardiac muscle NM_004047 ATP6V0B ATPase, H+ transporting, 1p32.3 DLPFC1.183 1.014 1.074 1.483* lysosomal 21 kDa, V0 subunit c″ NM_001696ATP6V1E1 ATPase, H+ transporting, 22pter-q11.2 DLPFC 1.138 1.694* 1.0810.939 lysosomal 31 kDa, V1 subunit E isoform 1 NM_004458 ACSL4 Acyl-CoAsynthetase long-chain Xq22.3-q23 DLPFC 1.165 1.266* 1.105 1.095 familymember 4 NM_174855 IDH3B Isocitrate dehydrogenase 3 20p13 DLPFC 1.1481.007 1.084 1.189* (NAD+) beta NM_133259 LRPPRC Leucine-rich PPR-motifcontaining 2p21 DLPFC 1.218 1.62* 1.164 1.802* NM_021107 MRPS12Mitochondrial ribosomal protein S12 19q13.1-q13.2 DLPFC 1.091 1.1401.110 1.276* NM_007103 NDUFV1 NADH dehydrogenase (ubiquinone) 11q13DLPFC 1.115 0.989 1.104 1.430* flavoprotein 1, 51 kDa NM_173157 NR4A1Nuclear receptor subfamily 4, 12q13 DLPFC 0.832 0.584* 0.895 0.516*group A, member 1 NM_000021 PSEN1 Presenilin 1 (Alzheimer disease 3)14q24.3 DLPFC 1.081 1.306* 0.882 0.825 NM_001183 ATP6AP1 ATPase, H+transporting, Xq28 AnCg 1.134 1.448 1.112 1.385 lysosomal accessoryprotein 1 NM_021979 HSPA2 Heat shock 70 kDa protein 2 14q24.1 AnCg 1.3602.552* 0.684 0.703 NM_174855 IDH3B Isocitrate dehydrogenase 3 20p13 AnCg1.136 0.998 1.099 0.985 (NAD+) beta NM_133259 LRPPRC Leucine-richPPR-motif containing 2p21 AnCg 1.198 1.079 1.08 1.023 NM_007103 NDUFV1NADH dehydrogenase (ubiquinone) 11q13 AnCg 1.169 1.480 1.148 1.107flavoprotein 1, 51 kDa NM_173157 NR4A1 Nuclear receptor subfamily 4,12q13 AnCg 0.833 0.599* 0.859 0.484* group A, member 1 NM_000021 PSEN1Presenilin 1 (Alzheimer disease 3) 14q24.3 AnCg 1.109 1.460* 0.845 1.089AK125435 PSMB1 Proteasome (prosome, macropain) 6q27 AnCg 1.271 1.615*1.020 1.162 subunit, beta type, 1 NM_002812 PSMD8 Proteasome (prosome,macropain) 19q13.2 AnCg 1.155 1.358* 1.104 1.231* 26S subunit,non-ATPase, 8

TABLE 22 QPCR QPCR MtDNA fold fold Encoded Brain change change start andCom- Hs. Accession Gene Symbol Region BPD MDD Description end bp Table 1plex Unigene AY882398 MtATP6 ATP6 DLPFC ATP synthase 0.853 0.876 Homosapiens 8528 . . . 9208 Mito paper V Hs.4509 F0 subunit 6 isolate Table11 20_U5a1(Tor13) (mt) mitochondrion, complete genome. AY882398 MtATP6ATP6 AnCg ATP synthase 0.588* 0.721* Homo sapiens 8528 . . . 9208 Mitopaper V Hs.4509 F0 subunit 6 isolate Table 11 20_U5a1(Tor13) (mt)mitochondrion, complete genome. AY882398 MtCO1 COX1 DLPFC cytochrome0.687 0.875 Homo sapiens 5905 . . . 7446 Mito paper IV Hs.4512 coxidase, isolate Table 11 subunit I 20_U5a1(Tor13) (mt) mitochondrion,complete genome. AY882398 MtCO1 COX1 AnCg cytochrome 0.527* 0.808 Homosapiens 5905 . . . 7446 Mito paper IV Hs.4512 c oxidase, isolate Table11 subunit I 20_U5a1(Tor13) (mt) mitochondrion, complete genome.AY882398 MtCO2 COX2 DLPFC cytochrome 0.836 1.078 Homo sapiens 7587 . . .8270 Mito paper IV Hs.4513 c oxidase, isolate Table 11 subunit II20_U5a1(Tor13) (mt) mitochondrion, complete genome. AY882398 MtCO2 COX2AnCg cytochrome 0.758# 0.895 Homo sapiens 7587 . . . 8270 Mito paper IVHs.4513 c oxidase, isolate Table 11 subunit II 20_U5a1(Tor13) (mt)mitochondrion, complete genome. AY882398 MtND1 ND1 DLPFC NADH 0.563#1.007 Homo sapiens 3308 . . . 4264 Mito paper I Hs.4535 dehydrogenase,isolate Table 11 subunit I 20_U5a1(Tor13) (mt) mitochondrion, completegenome. AY882398 MtND1 ND1 AnCg NADH 0.855 0.957 Homo sapiens 3308 . . .4264 Mito paper I Hs.4535 dehydrogenase, isolate Table 11 subunit I20_U5a1(Tor13) (mt) mitochondrion, complete genome. AY882398 MtND2 ND2DLPFC NADH 0.539 0.921 Homo sapiens 4471 . . . 5514 Mito paper I Hs.4536dehydrogenase, isolate Table 11 subunit II 20_U5a1(Tor13) (mt)mitochondrion, complete genome. AY882398 MtND3 ND3 DLPFC NADH 1.0740.856 Homo sapiens 10060 . . . 10405 Mito paper I Hs.4537 dehydrogenase,isolate Table 11 subunit III 20_U5a1(Tor13) (mt) mitochondrion, completegenome. AY882398 MtND3 ND3 AnCg NADH 0.752# 0.918 Homo sapiens 10060 . .. 10405 Mito paper I Hs.4537 dehydrogenase, isolate Table 11 subunit III20_U5a1(Tor13) (mt) mitochondrion, complete genome. AY882398 MtATP6 ATP6DLPFC ATP synthase 0.853 0.876 Homo sapiens 8528 . . . 9208 Mito paper VHs.4509 F0 subunit 6 isolate Table 11 20_U5a1(Tor13) (mt) mitochondrion,complete genome.*significant at p < 0.05 two-tailed#trend p < 0.1 two-tailed

TABLE 23 Primer Forward Reverse VASE 5′-GACCCCATTCCCTCCATCAC-3′5′-GGCTACGCACCACCATGTG-3′ Exon a 5″-GACGCAGCCAGTCCATAGC-3′ *1 Exon b5′-CGTCTACCCCTGTTCCATTGTC-3′ 5′-TCTGGTGGAGACAATGGAACAG-3′ Exon c5′-TCCTGCCCTTGCAACCA-3′ 5′-GGTTGCAAGGGCAGGAAGA-3′ SEC exon5′-CCAAGCTGGTCTTCATAATGCTCTA-3′ 5′TTTGATGCTTGAACACTATGAACATG-3′ Exon 35′-GGCGGCGCTCAATGG-3′ *2 Exon 8 *3 5′-GATCAGGTTCACTTTAATAGAGTTTCCA-3′SNP9 for sequencing 5′-CGCAGCCAGTCCGTAAGTAAAG-3′5′-AAGCTGGACCGGCTACTAGGA-3′

TABLE 24 Tests For Genotypic Association (Risk Allele 1) HeterozygousHomozygous Allele Positivity Odds Ratio [C.I.] χ² (p-value) Odds Ratio[C.I.] χ² (p-value) Odds Ratio [C.I.] χ² (p-value) SNP 9 A/A<->C/AC/C<->A/A [C/C + C/A]<->A/A SZ 0.054 [0.003-1.16]  6.6 (0.01) 9.57[0.47-193.92] 3.86 (0.049) 0.084 [0.004-1.67] 4.88 (0.027) SNP bC/C<->T/C T/T<->C/C [T/T + T/C]<->C/C BPD  4.05 [1.16-14.12] 5.33 (0.02)2.97 [0.78-11.30] 2.65 (0.103)  3.66 [1.08-11.30] 4.81 (0.028)

TABLE 25 Haplotype Frequency (Odds Ratio) SNP 9 − SNP b Control BPD* SZ#C − T 0.2 0.19 (0.95) 0.31 (1.54) C − (T/C) 0.31 0.46 (1.48) 0.37 (1.19)(C/A) − (T/C) 0.22 0.21 (0.95) 0.11 (0.50) p (value) *BPD vs Control<0.0001 # SZ vs Control <0.0001 SZ vs BPD 0.0003

TABLE 26 Genotype Allele Counts p (Fisher's Polymorphism n Counts(Frequency) (Frequency) exact test) SNP 9 C/C C/A A/A C A Control 55 33(0.60) 22 (0.40)  0 (0)  88 (0.80) 22 (0.20) BPD 70 47 (0.67) 23 (0.33) 0 (0) 117 (0.84) 23 (.16) 0.466 SZ 35 24 (0.69)  8 (0.23)  3 (0.09)  56(0.80) 14 (0.20) 1 BPD + SZ 105 71 (0.68) 31 (0.30)  3 (0.02) 173 (0.82)37 (0.18) 0.602 SNP b T/T T/C C/C T C Control 55 16 (0.29) 29 (0.53) 10(0.18)  61 (0.55) 49 (0.45) BPD 70 19 (0.27) 47 (0.67)  4 (0.06)  85(0.61) 55 (.39) 0.402 SZ 35 13 (0.37) 19 (0.54)  3 (0.09)  45 (0.64) 25(0.36) 0.24 BPD + SZ 105 32 (0.30) 66 (0.63)  7 (0.07) 130 (0.62) 80(0.38) 0.264

TABLE 27 SNP Genotype Splice Variant BPD vs C MDD vs C SNP 9 C/C a-b-c0.052 ↑ SNP 6 G/C b-c-SEC 0.05 ↑  SNP b T/T VASE (−) 0.056 ↑ SNP b T/Cc-SEC 0.013 ↓ SNP b T/C NCAM1 Ct Q-PCR 0.053 ↑

TABLE 28.1 UG Cluster Symbol Gene Name Cytoband fc_AnCg Hs.5490381.919839205 Hs.547062 Transcribed locus 1.773637669 Hs.483454 CNN3Calponin 3, acidic 1p22-p21 1.71410127 Hs.534365 ZNF43 Zinc fingerprotein 43 (HTF6) 19p13.1-p12 1.653473114 Hs.534314 EIF5A Eukaryotictranslation initiation factor 5A 17p13-p12 1.616760481 Hs.427236Transcribed locus 1.57275662 Hs.336957 ZNF479 Zinc finger protein 4797p11.2 1.561114027 Hs.534385 THOC4 THO complex 4 17q25.3 1.545094715Hs.114084 ENPP7 Ectonucleotide pyrophosphatase/phosphodiesterase 717q25.3 1.490770143 Hs.315369 AQP4 Aquaporin 4 18q11.2-q12.1 1.478027231Hs.370410 KIAA1145 KIAA1145 protein 12q22 1.435347843 Hs.75914 RNP24Coated vesicle membrane protein 12q24.31 1.419831899 Hs.406708 ILT7Leukocyte immunoglobulin-like receptor, subfamily A 19q13.4 1.410439598(without TM domain), member 4 Hs.234249 MAPK8IP1 Mitogen-activatedprotein kinase 8 interacting protein 1 11p12-p11.2 1.371562585 Hs.534525LOC114984 Hypothetical protein BC014089 16p13.3 1.368785293 Hs.212838A2M Alpha-2-macroglobulin 12p13.3-p12.3 1.365561844 Hs.402752 TAF15TAF15 RNA polymerase II, TATA box binding protein 17q11.1-q11.21.362205401 (TBP)-associated factor, 68 kDa Hs.535415 Ig rearrangedgamma-chain mRNA, subgroup VH2, V-D-J region 1.355666889 Hs.467138Transcribed locus, moderately similar to XP_507997.1 1.351924341 similarto Kv channel interacting protein 2 isoform 4; A-type potassium channelmodulatory protein 2; cardiac voltage gated potassium channel modulatorysubunit; Kv channel- interacting protein 2 [Pan tr Hs.513600 Transcribedlocus 1.347512479 Hs.380218 Transcribed locus 1.327051286 Hs.458607 NOPELikely ortholog of mouse neighbor of Punc E11 15q22.31 1.324220424Hs.42034 TCP10L T-complex 10 (mouse)-like 21q22.11 1.322514626 Hs.521286RARRES2 Retinoic acid receptor responder (tazarotene induced) 2 7q36.11.31025151 Hs.25422 CDNA FLJ42519 fis, clone BRACE3000787 1.309835897Hs.293379 Transcribed locus 1.307793259 Hs.356766 Similar to RPE-spondin20q13.13 1.290259345 Hs.379010 PSCA Prostate stem cell antigen 8q24.21.287232595 Hs.511757 GJB6 Gap junction protein, beta 6 (connexin 30)13q11-q12.1 1.287226239 Hs.59106 CGRRF1 Cell growth regulator with ringfinger domain 1 14q22.2 1.284552431 Hs.83916 NDUFA5 NADH dehydrogenase(ubiquinone) 1 alpha subcomplex, 5, 13 kDa 7q32 1.283862892 Hs.119878FLJ34389 Hypothetical protein FLJ34389 16q22.3 1.28271805 Hs.494261PSAT1 Phosphoserine aminotransferase 1 9q21.2 1.276727208 Hs.75969 PNRC1Proline-rich nuclear receptor coactivator 1 6q15 1.273555895 Hs.467273CACNG8 Calcium channel, voltage-dependent, gamma subunit 8 19q13.41.270119391 Hs.280805 MGC20579 Hypothetical protein MGC20579 13q341.269164507 Hs.145480 Transcribed locus 1.266189386 Hs.511454 PLXNA4Plexin A4 7q32.3 1.263673467 Hs.80132 SNX15 Sorting nexin 15 11q121.26259913 Hs.514819 AP2B1 Adaptor-related protein complex 2, beta 1subunit 17q11.2-q12 1.250901951 Hs.385772 LOC283914 Hypothetical proteinLOC283914 16p11.1 1.247941693 Hs.151536 RAB13 RAB13, member RAS oncogenefamily 1q21.2 1.247404054 Hs.548424 Transcribed locus 1.245303451Hs.519930 C6orf62 Chromosome 6 open reading frame 62 6p22.2 1.233111115Hs.45140 TMEM35 Transmembrane protein 35 Xq22.1 1.232645678 Hs.505295MADP-1 MADP-1 protein 12q12 1.226870897 Hs.513883 PELP1 Proline-,glutamic acid-, leucine-rich protein 1 17p13.2 1.224880728 Hs.474836LOC387593 TPTE/TPIP pseudogene 22q13 1.223415544 Hs.115284 ZNF213 Zincfinger protein 213 16p13.3 1.223309419 Hs.369624 15E1.2 Hypotheticalprotein 15E1.2 12q24.31 1.223144605 Hs.467960 RAB10 RAB10, member RASoncogene family 2p23.3 1.222273799 Hs.533282 NONO Non-POU domaincontaining, octamer-binding Xq13.1 1.219220007 Hs.181272 PKD2 Polycystickidney disease 2 (autosomal dominant) 4q21-q23 1.212879872 Hs.80720 GAB1GRB2-associated binding protein 1 4q31.21 1.211569918 Hs.123464 P2RY5Purinergic receptor P2Y, G-protein coupled, 5 13q14 1.210914564Hs.507185 ZFPM1 Zinc finger protein, multitype 1 16q24.2 1.210160133Hs.5324 C2orf25 Chromosome 2 open reading frame 25 2q23.3 1.209212561Hs.374847 LOC400794 Hypothetical gene supported by BC030596 1q23.21.208951568 Hs.517792 C3orf10 Chromosome 3 open reading frame 10 3p25.31.208760837 Hs.517352 PRODH Proline dehydrogenase (oxidase) 1 22q11.211.206253745 Hs.483561 ORF1-FL49 Putative nuclear protein ORF1-FL495q31.2 1.205748855 Hs.75640 NPPA Natriuretic peptide precursor A 1p36.211.20542617 Hs.491695 UBE2V2 Ubiquitin-conjugating enzyme E2 variant 28q11.21 1.204850064 Hs.335057 NEDD5 Neural precursor cell expressed,developmentally 2q37 1.202774491 down-regulated 5 Hs.28280 SLC35F4Solute carrier family 35, member F4 14q22.2 1.201026204

TABLE 28.2 UG Cluster Symbol Gene Name Cytoband fc_AnCg Hs.134974 GAP43Growth associated protein 43 3q13.1-q13.2 0.833001805 Hs.444637 LRP8 Lowdensity lipoprotein receptor-related protein 8, apolipoprotein 1p340.832591468 e receptor Hs.268849 GLO1 Glyoxalase I 6p21.3-p21.10.832479968 Hs.435952 CDK5RAP1 CDK5 regulatory subunit associatedprotein 1 20pter-q11.23 0.831820461 Hs.360940 dJ222E13.1 Kraken-like22q13 0.828943053 Hs.500721 MMS19L MMS19-like (MET18 homolog, S.cerevisiae) 10q24-q25 0.827060597 Hs.200285 TCF4 Transcription factor 418q21.1 0.826908526 Hs.2890 PRKCG Protein kinase C, gamma 19q13.40.82630472 Hs.153661 Transcribed locus 0.825857073 Hs.483924 MRPL22Mitochondrial ribosomal protein L22 5q33.1-q33.3 0.825300862 Hs.210385HERC1 Hect (homologous to the E6-AP (UBE3A) carboxyl terminus) 15q220.82523312 domain and RCC1 (CHC1)-like domain (RLD) 1 Hs.353454 FLJ10276Hypothetical protein FLJ10276 1p35.1 0.825093453 Hs.157234 MRNA; cDNADKFZp547A0515 (from clone DKFZp547A0515) 0.824586185 Hs.75667 SYPSynaptophysin Xp11.23-p11.22 0.824282156 Hs.451353 Homo sapiens, cloneIMAGE: 5288537, mRNA 0.823552515 Hs.514373 MTMR4 Myotubularin relatedprotein 4 17q22-q23 0.823152304 Hs.102696 MCTS1 Malignant T cellamplified sequence 1 Xq22-q24 0.822759185 Hs.445503 SYN2 Synapsin II3p25 0.822588683 Hs.524094 PS1D Putative S1 RNA binding domain protein1p35.2 0.822570466 Hs.522668 UBQLN2 Ubiquilin 2 Xp11.23-p11.10.821156426 Hs.517148 TH1L TH1-like (Drosophila) 20q13 0.821107397Hs.380334 ZNF148 Zinc finger protein 148 (pHZ-52) 3q21 0.821027253Hs.534575 MGC2198 Hypothetical protein MGC2198 5q35.2 0.819426558Hs.47546 C6orf70 Chromosome 6 open reading frame 70 6q27 0.819049461Hs.25601 CHD3 Chromodomain helicase DNA binding protein 3 17p13.10.818740301 Hs.460978 APPBP1 Amyloid beta precursor protein bindingprotein 1, 59 kDa 16q22 0.818504577 Hs.448851 USP6 Ubiquitin specificprotease 6 (Tre-2 oncogene) 17q11 0.818420142 Hs.532755 GTL3 Likelyortholog of mouse gene trap locus 3 16q21 0.816593983 Hs.98510 WDR44 WDrepeat domain 44 Xq24 0.815070227 Hs.189119 CXXC5 CXXC finger 5 5q31.20.814065874 Hs.134060 FNBP1L Formin binding protein 1-like 1p22.10.813237448 Hs.549821 Data not found 0.812556603 Hs.78944 RGS2 Regulatorof G-protein signalling 2, 24 kDa 1q31 0.811942329 Hs.535060 LOC4413859p24.1 0.811837917 Hs.549166 Data not found 0.811572937 Hs.224418Transcribed locus 0.811556308 Hs.5258 MAGED1 Melanoma antigen, family D,1 Xp11.23 0.811035568 Hs.537449 Transcribed locus 0.810141577 Hs.515545TBC1D17 TBC1 domain family, member 17 19q13.33 0.809453648 Hs.268122LOC51321 Hypothetical protein LOC51321 17q24.2 0.808975121 Hs.502910NKIRAS2 NFKB inhibitor interacting Ras-like 2 17q21.2 0.808919755Hs.471876 ING5 Inhibitor of growth family, member 5 2q37.3 0.806159689Hs.198612 GPR51 G protein-coupled receptor 51 9q22.1-q22.3 0.806097527Hs.401509 RBM10 RNA binding motif protein 10 Xp11.23 0.806076882Hs.380857 TD-60 RCC1-like 1p36.13 0.805526827 Hs.49582 PPP1R12A Proteinphosphatase 1, regulatory (inhibitor) subunit 12A 12q15-q21 0.805427552Hs.515162 CALR Calreticulin 19p13.3-p13.2 0.804252658 Hs.444558 KHDRBS3KH domain containing, RNA binding, signal transduction 8q24.20.803823019 associated 3 Hs.317632 CDH18 Cadherin 18, type 25p15.2-p15.1 0.803613164 Hs.471104 NOP5/NOP58 Nucleolar proteinNOP5/NOP58 2q33.1 0.802352232 Hs.348526 LOC474358 Hypothetical BC042079locus 10q23-q25 0.802291667 Hs.475018 TCF20 Transcription factor 20(AR1) 22q13.3 0.801897074 Hs.463074 ATP6V0A1 ATPase, H+ transporting,lysosomal V0 subunit a isoform 1 17q21 0.801766875 Hs.28144 FSD1Fibronectin type 3 and SPRY domain containing 1 19p13.3 0.800329999Hs.32309 INPP1 Inositol polyphosphate-1-phosphatase 2q32 0.796446965Hs.512973 HSPC121 Butyrate-induced transcript 1 15q22.2 0.796376497Hs.13245 LPPR4 Plasticity related gene 1 1p21.3 0.794472742 Hs.199743ME3 Malic enzyme 3, NADP(+)-dependent, mitochondrial 11cen-q22.30.794075417 Hs.523755 FLRT1 Fibronectin leucine rich transmembraneprotein 1 11q12-q13 0.792664481 Hs.515785 BLVRB Biliverdin reductase B(flavin reductase (NADPH)) 19q13.1-q13.2 0.792511112 Hs.437277 MGAT4BMannosyl (alpha-1,3-)-glycoprotein beta-1,4-N- 5q35 0.790721678acetylglucosaminyltransferase, isoenzyme B Hs.387982 CDNA clone IMAGE:5261489, partial cds 0.789879979 Hs.136164 TSPYL2 TSPY-like 2 Xp11.20.788609957 Hs.332847 CRIM1 Cysteine-rich motor neuron 1 2p210.786568887 Hs.348493 GPRASP2 G protein-coupled receptor associatedsorting protein 2 Xq22.1 0.786263129 Hs.7736 MRPL27 Mitochondrialribosomal protein L27 17q21.3-q22 0.785613917 Hs.177275 ANKRD6 Ankyrinrepeat domain 6 6q14.2-q16.1 0.783389812 Hs.124015 HAGHLHydroxyacylglutathione hydrolase-like 16p13.3 0.782617204 Hs.79322 QARSGlutaminyl-tRNA synthetase 3p21.3-p21.1 0.781931967 Hs.158748 SLC35F3Solute carrier family 35, member F3 1q42.2 0.780681609 Hs.158460 CDK5R2Cyclin-dependent kinase 5, regulatory subunit 2 (p39) 2q35 0.779713574Hs.337730 LCMT1 Leucine carboxyl methyltransferase 1 16p12.3-16p12.10.777655555 Hs.282998 RBM9 RNA binding motif protein 9 22q13.10.775799713 Hs.60300 ZNF622 Zinc finger protein 622 5p15.1 0.775473024Hs.405590 EIF3S6 Eukaryotic translation initiation factor 3, subunit 648 kDa 8q22-q23 0.775166314 Hs.373952 CAMTA2 Calmodulin bindingtranscription activator 2 17p13.2 0.775135303 Hs.528187 Hypotheticalgene supported by AK096649 2q33.1 0.774877993 Hs.536326 Transcribedlocus 0.774173869 Hs.532231 COPG2 Coatomer protein complex, subunitgamma 2 7q32 0.773663441 Hs.114169 LRRTM2 Leucine rich repeattransmembrane neuronal 2 5q31.3 0.773056562 Hs.496267 IGBP1Immunoglobulin (CD79A) binding protein 1 Xq13.1-q13.3 0.771399953Hs.190722 HSPC142 HSPC142 protein 19p13.11 0.770969106 Hs.130197KIAA1889 KIAA1889 protein 8q12.1 0.770498302 Hs.436446 ARMETArginine-rich, mutated in early stage tumors 3p21.1 0.769942554Hs.381300 MGC57858 Hypothetical protein MGC57858 6p21.31 0.769698647Hs.33191 UNC5A Unc-5 homolog A (C. elegans) 5q35.2 0.769489374 Hs.350065PLXNA2 Plexin A2 1q32.2 0.767903428 Hs.48372 Full length insert cDNAclone YZ87G11 0.766810973 Hs.3797 RAB26 RAB26, member RAS oncogenefamily 16p13.3 0.765394204 Hs.21925 Transcribed locus 0.764561674Hs.336588 LOC147670 Hypothetical protein LOC147670 19q13.43 0.763351376Hs.78466 PSMD8 Proteasome (prosome, macropain) 26S subunit, non-ATPase,8 19q13.2 0.76234581 Hs.121520 AMIGO2 Amphoterin induced gene 2 12q13.110.760653807 Hs.443731 USP8 Ubiquitin specific protease 8 15q21.20.75760815 Hs.171501 USP11 Ubiquitin specific protease 11 Xp11.230.755609225 Hs.187861 THRB Thyroid hormone receptor, beta(erythroblastic leukemia viral (verb- 3p24.3 0.755503889 a) oncogenehomolog 2, avian) Hs.272284 SLITRK4 SLIT and NTRK-like family, member 4Xq27.3 0.755411535 Hs.509736 HSPCB Heat shock 90 kDa protein 1, beta6p12 0.755057388 Hs.188594 Transcribed locus 0.755026908 Hs.497806 MARK1MAP/microtubule affinity-regulating kinase 1 1q41 0.751792399 Hs.549761Data not found 0.749944 Hs.479867 CENPC1 Centromere protein C 14q12-q13.3 0.749713558 Hs.135736 NGL-1 Netrin-G1 ligand 11p120.747993997 Hs.463466 CA10 Carbonic anhydrase X 17q21 0.746516358Hs.143587 Transcribed locus 0.745018326 Hs.549196 Data not found0.744120055 Hs.534913 Hypothetical gene supported by BC019717 16p11.20.743499122 Hs.523550 ZNF364 Zinc finger protein 364 1q21.1 0.742420643Hs.90242 Homo sapiens, clone IMAGE: 4796172, mRNA 0.741848633 Hs.475150KIAA0767 KIAA0767 protein 22q13.31 0.741559246 Hs.530698 CHD8Chromodomain helicase DNA binding protein 8 14q11.2 0.738476834 Hs.55879ABCC10 ATP-binding cassette, sub-family C (CFTR/MRP), member 10 6p21.10.738455293 Hs.323537 FLJ12953 Hypothetical protein FLJ12953 similar toMus musculus D3Mm3e 2p13.1 0.737391028 Hs.301296 CDNA: FLJ23131 fis,clone LNG08502 0.737354551 Hs.502461 DGKZ Diacylglycerol kinase, zeta104 kDa 11p11.2 0.734852399 Hs.471096 ALS2 Amyotrophic lateral sclerosis2 (juvenile) 2q33.1 0.73175125 Hs.92732 PDZK4 PDZ domain containing 4Xq28 0.727016153 Hs.537841 Transcribed locus 0.726748437 Hs.7744 NDUFV1NADH dehydrogenase (ubiquinone) flavoprotein 1, 51 kDa 11q13 0.726496223Hs.100890 RPRM Reprimo, TP53 dependant G2 arrest mediator candidate2q23.3 0.719810824 Hs.6132 CPNE6 Copine VI (neuronal) 14q11.20.718586854 Hs.412019 C6orf80 Chromosome 6 open reading frame 806q23.1-q24.1 0.715749314 Hs.119594 CIT Citron (rho-interacting,serine/threonine kinase 21) 12q24 0.712998565 Hs.518460 AP2M1Adaptor-related protein complex 2, mu 1 subunit 3q28 0.709632072Hs.65425 CALB1 Calbindin 1, 28 kDa 8q21.3-q22.1 0.70924145 Hs.479116SH3TC1 SH3 domain and tetratricopeptide repeats 1 4p16.1 0.704347818Hs.173859 FZD7 Frizzled homolog 7 (Drosophila) 2q33 0.697933574Hs.363137 ACAT2 Acetyl-Coenzyme A acetyltransferase 2 (acetoacetylCoenzyme 6q25.3-q26 0.695447549 A thiolase) Hs.153648 PPFIA4 Proteintyrosine phosphatase, receptor type, f polypeptide 1q32.1 0.694615615(PTPRF), interacting protein (liprin), alpha 4 Hs.524071 Transcribedlocus, strongly similar to XP_084672.3 similar to 0.691986755 CDNAsequence BC021608 [Homo sapiens] Hs.506784 LNK Lymphocyte adaptorprotein 12q24 0.688023619 Hs.516617 SATB2 SATB family member 2 2q330.681642635 Hs.23406 KCTD4 Potassium channel tetramerisation domaincontaining 4 13q14.12 0.676435668 Hs.220950 FOXO3A Forkhead box O3A 6q210.669990152 Hs.370549 BCL11A B-cell CLL/lymphoma 11A (zinc fingerprotein) 2p16.1 0.654002694 Hs.483239 ALDH7A1 Aldehyde dehydrogenase 7family, member A1 5q31 0.651849727 Hs.445733 GSK3B Glycogen synthasekinase 3 beta 3q13.3 0.647879909 Hs.268515 MN1 Meningioma (disrupted inbalanced translocation) 1 22q11 0.64462122 Hs.319503 PTCHD1 Patcheddomain containing 1 Xp22.11 0.644497163 Hs.106511 PCDH17 Hypotheticalprotein LOC144997 13q21.1 0.644270897 Hs.91448 DUSP14 Dual specificityphosphatase 14 17q12 0.639891125 Hs.448041 FLJ32363 FLJ32363 protein5p12 0.633100428 Hs.22584 PDYN Prodynorphin 20pter-p12 0.630525299Hs.215839 DLG2 Discs, large homolog 2, chapsyn-110 (Drosophila) 11q210.620144715 Hs.11899 HMGCR 3-hydroxy-3-methylglutaryl-Coenzyme Areductase 5q13.3-q14 0.619486994 Hs.23539 CDNA FLJ42249 fis, cloneTKIDN2007667 0.614085673 Hs.314436 NEDL2 NEDD4-related E3 ubiquitinligase NEDL2 2q32.3 0.605505392 Hs.490294 KIAA1549 KIAA1549 protein 7q340.548338996 Hs.518469 FLJ10560 Hypothetical protein FLJ10560 3q27.30.498445319 Hs.546322 NOL4 Nucleolar protein 4 18q12 0.491050809Hs.282177 PIP5K1C Phosphatidylinositol-4-phosphate 5-kinase, type I,gamma 19p13.3 0.490622069 Hs.2785 KRT17 Keratin 17 17q12-q21 0.474185311Hs.536506 Transcribed locus 0.467413109 Hs.435001 KLF10 Kruppel-likefactor 10 8q22.2 0.463636382 Hs.537539 Transcribed locus 0.358666831

TABLE 29 v-ATPase Human MDD vs Monkey stressed Array Results HumanT-test Human T-test Monkey Affy HIP illu HIP Midlife Stress UGRepAccName Symbol t2hcmdd.affy tHCMdd.illu change BQ230447 ATPase, H+transporting, lysosomal ATP6V0E −2.8565 −2.2254 −1.07 9 kDa, V0 subunite AF245517 ATPase, H+ transporting, lysosomal ATP6V0A4 −1.6935 −1.52081.01 V0 subunit a isoform 4 NM_012463 ATPase, H+ transporting, lysosomalATP6V0A2 −0.8322 −1.6802 −1.05 V0 subunit a isoform 2 CR607789 ATPase,H+ transporting, lysosomal ATP6V1G1 −0.0535 −0.0440 −1.08 13 kDa, V1subunit G isoform 1 AK127853 ATPase, H+ transporting, lysosomal ATP6V1B10.3202 −0.8313 1.02 56/58 kDa, V1 subunit B, isoform 1 (Renal tubularacidosis with deafness) BF214530 ATPase, H+ transporting, lysosomalATP6V1E1 1.3703 1.9643 −1.01 31 kDa, V1 subunit E isoform 1 AK024101ATPase, H+ transporting, lysosomal ATP6V1D 1.6380 2.6589 1.09 34 kDa, V1subunit D NM_001690 ATPase, H+ transporting, lysosomal ATP6V1A 1.78372.4222 1.15 70 kDa, V1 subunit A NM_001695 ATPase, H+ transporting,lysosomal ATP6V1C1 1.7882 1.0692 −1.01 42 kDa, V1 subunit C, isoform 1AK128641 ATPase, H+ transporting, lysosomal ATP6V0D1 1.8249 2.4330 1.0338 kDa, V0 subunit d isoform 1 BC053601 ATPase, H+ transporting,lysosomal ATP6V0B 1.8268 −0.2217 1.10 21 kDa, V0 subunit c″ AK127505ATPase, H+ transporting, lysosomal ATP6V0C 2.5856 2.2705 −1.04 16 kDa,V0 subunit c NM_001693 ATPase, H+ transporting, lysosomal ATP6V1B22.6827 2.6120 1.04 56/58 kDa, V1 subunit B, isoform 2 AK125927 ATPase,H+ transporting, lysosomal ATP6V0A1 3.3021 1.2269 1.04 V0 subunit aisoform 1

TABLE 30 Probe Set AII AD AII AD AII CUS + AII CUS + Name IdentifierLocusLink Name H2O Ave CUS Ave CUS T CUS FC AD T AD FC 1370043_atNM_031753 79559 activated leukocyte 8.554991091 8.737278 0.3055171.134681103 −0.337997115 0.87551622 cell adhesion molecule 1375424_atBE107525 64040 aldehyde 7.7269596 7.985884 0.253566 1.196585931−0.275888751 0.815851533 dehydrogenase family 9, subfamily A1 1370176_atBG378620 171086 amyotrophic lateral 8.289171999 8.644384 0.5492871.279173789 −0.422598222 0.816014485 sclerosis 2 (juvenile) chromosomeregion, candidate 3 1370050_at NM_053311 29598 ATPase, Ca++ 10.0215640610.47301 0.407594 1.367412006 −0.303601287 0.776657575 transporting,plasma membrane 1 1367585_a_at M28647 24211 ATPase, Na+K+ 10.8667748210.70967 −0.27986 0.896825718 0.365553735 1.117986929 transporting,alpha 1 1398781_at NM_053884 116664 ATPase, vacuolar, 9.7947088879.635878 −0.40588 0.895750971 0.501130634 1.131514226 14 kD 1367595_s_atNM_012512 24223 Beta-2- 10.16168978 9.88582 −0.59779 0.8259522610.384629381 1.135862492 microglobulin 1370074_at NM_057196 117542brain-specific 8.394268852 8.230674 −0.55098 0.892797502 0.4670620821.118839281 angiogenesis inhibitor 1- associated protein 2 1369993_atNM_133605 171140 calcium/calmodulin- 8.242780231 8.480603 0.3388881.179211766 −0.292444973 0.860882267 dependent protein kinase (CaMkinase) II gamma 1389824_at BF404381 25400 calcium/calmodulin-7.810218827 7.950381 0.416069 1.102029271 −0.470849794 0.896960966dependent protein kinase II alpha subunit 1398251_a_at NM_021739 24245calcium/calmodulin- 8.228441025 8.843395 0.474736 1.531509499−0.367083116 0.701179029 dependent protein kinase II beta subunit1367462_at U10861 29156 calpain, small 9.116789268 8.937121 −0.508860.882905842 0.648775676 1.158940404 subunit 1 1389876_at BE111167 287005CaM-kinase II 8.411415385 8.683458 0.388539 1.207516219 −0.3313930940.833810939 inhibitor alpha 1370853_at AA858621 287005 CaM-kinase II9.552520138 9.824481 0.484035 1.207447775 −0.302368972 0.879487359inhibitor alpha 1369215_a_at NM_012836 25306 carboxypeptidase D7.60221365 7.851067 0.409687 1.188262417 −0.318247147 0.8658834981389974_at BF555171 116549 casein kinase II, 7.070655253 7.336550.576709 1.20238131 −0.509595002 0.849661157 alpha 1 polypeptide1387436_at NM_022616 64551 CDC10 (cell 8.264076026 7.838606 −0.822820.744596339 0.558756443 1.170398833 division cycle 10, S. cerevisiae,homolog) 1370922_at L15011 29145 cortexin 10.52034023 10.29252 −0.390420.853925826 0.642216784 1.297259097 1368059_at NM_053955 117024crystallin, mu 9.15043777 8.934658 −0.55932 0.861080678 0.407261881.109586413 1370438_at AF037071 192363 C-terminal PDZ 8.4781066438.941752 0.528156 1.37902155 −0.286782718 0.819872562 domain ligand ofneuronal nitric oxide synthase 1370810_at L09752 64033 cyclin D27.552338207 7.824805 0.627432 1.207871164 −0.510232497 0.8563515781370180_at AA891213 94267 diphosphoinositol 9.720407691 9.551001−0.32062 0.889208564 0.33907154 1.112564538 polyphosphatephosphohydolase type II 1399090_at AA944459 252902 dynein, 8.7089703259.160194 0.592983 1.36719938 −0.611477208 0.713171499 cytoplasmic, lightintermediate chain 1 1370048_at NM_053936 116744 endothelial 8.1908740368.434857 0.460008 1.184257781 −0.276403406 0.88926266 differentiation,lysophosphatidic acid G-protein- coupled receptor, 2 1370341_at AF01997324334 enolase 2, gamma 10.25966095 10.09239 −0.27444 0.8905283860.511287186 1.226632739 1367958_at NM_024397 79249 eps8 binding7.501336434 7.734993 0.390605 1.175811622 −0.214182288 0.899358171protein (e3B1), alternatively spliced 1373067_at AI102738 ESTs9.097780684 9.795279 0.560829 1.621690153 −0.394405591 0.6911673361375687_at BE097926 ESTs 9.102908418 9.589148 0.67554 1.400788553−0.668809291 0.710828697 1375343_at BE116572 ESTs 9.636710979 10.055690.637477 1.336979858 −0.600017235 0.721789025 1390722_at AW531272 ESTs8.052433351 8.445177 0.563541 1.312887882 −0.564580433 0.7376657961371776_at AA819268 ESTs 8.792612117 9.070286 0.439984 1.21223885−0.60941328 0.751754214 1377029_at AI235414 ESTs 7.519789299 8.0664210.538435 1.460671268 −0.347221628 0.758851202 1374002_at AI045904 ESTs7.891491864 8.3451 0.66405 1.369460535 −0.489475041 0.7737848921372183_at AI230596 ESTs 7.499883481 7.870917 0.59093 1.293279024−0.538050749 0.787917813 1390100_s_at BG371810 ESTs 8.847513531 9.3353070.623353 1.402298615 −0.383584226 0.796768397 1376463_at AA955579 ESTs8.580618929 8.884818 0.477979 1.234732891 −0.512299476 0.7979640771380433_at AI229240 ESTs 8.198656524 8.544649 0.807649 1.271025354−0.703481364 0.812645109 1376911_at BM386385 ESTs 8.998969791 9.3042560.378751 1.235663347 −0.292496741 0.834798828 1374276_at BE104102 ESTs8.042219162 8.352924 0.479598 1.24031378 −0.357883889 0.8433066331393268_at AI071071 ESTs 7.760844879 8.008586 0.670383 1.187346647−0.604731486 0.847734973 1385889_at AA893212 ESTs 7.456567924 7.6811230.541819 1.168417012 −0.524932857 0.856389756 1388985_at AI012869 ESTs10.3902729 10.71161 0.771777 1.249486875 −0.374963851 0.8613370251375144_at BM388843 ESTs 9.305640348 9.77995 0.689094 1.389253394−0.247358915 0.862096412 1375850_at BG371810 ESTs 10.32943696 10.59070.646492 1.198530654 −0.463027833 0.863301098 1376685_at AW532489 ESTs7.03405558 7.31854 0.585335 1.217975253 −0.362402037 0.8739637771375538_at AI230737 ESTs 7.60108064 7.77676 0.590257 1.129495994−0.611495294 0.87898368 1377232_at BF406608 ESTs 7.50385238 7.6499130.456061 1.106543988 −0.555511902 0.885897068 1374485_at AI137762 ESTs7.635036986 7.803592 0.478724 1.123932187 −0.480827091 0.885977411389104_s_at BF388420 ESTs 7.793627056 7.97877 0.44046 1.136929557−0.340035773 0.897093342 1372790_at BG671530 ESTs 9.913991148 9.6554−0.42594 0.835903569 0.333317197 1.121671745 1388738_at AI411227 ESTs9.013127784 8.836253 −0.32841 0.884617394 0.421781411 1.1340023231389600_at AW524433 ESTs 9.341707252 9.136027 −0.31744 0.8671297370.294052169 1.146455757 1388195_at AW140475 ESTs 8.841214015 8.623431−0.48629 0.859885815 0.493109601 1.177343855 1389867_at BI281086 ESTs9.622618423 9.295352 −0.44041 0.797045168 0.527626149 1.3253641711371977_at BG381477 ESTs, Highly 8.22534466 7.988656 −0.432380.848690922 0.274472639 1.102307933 similar to actin related protein 2/3complex, subunit 3 (21 kDa); Arp2/3 complex subunit p21-Arc [Musmusculus] [M. musculus] 1388683_at AI411174 ESTs, Highly 8.669630728.511747 −0.43469 0.896338715 0.466659704 1.111224693 similar tohypothetical protein MGC14151 [Homo sapiens] [H. sapiens] 1375245_atAA800669 ESTs, Highly 10.09883803 9.917245 −0.40076 0.8817289330.482696461 1.136988127 similar to A36180 61K transforming protein -human [H. sapiens] 1383054_at BE111631 ESTs, Highly 7.47092638 7.6914870.684678 1.165186416 −0.438439828 0.895791948 similar to I48724 zincfinger protein PZF - mouse [M. musculus] 1389957_at BG378149 ESTs,Highly 9.604565474 9.852639 0.339593 1.187620315 −0.23684341 0.879305448similar to JW0059 mtprd protein - mouse [M. musculus] 1374593_atAA799421 ESTs, Highly 8.436415302 8.757416 0.610494 1.249196498−0.371471138 0.855707419 similar to KPCE_RAT PROTEIN KINASE C, EPSILONTYPE (NPKC-EPSILON) [R. norvegicus] 1375119_at BI284798 ESTs, Highly9.262421398 9.747071 0.469691 1.399245716 −0.269750886 0.795573103similar to S70642 ubiquitin ligase Nedd4 - rat (fragment) [R.norvegicus] 1375305_at BI282028 ESTs, Highly 10.64049686 10.866510.543331 1.169598117 −0.407433833 0.884962553 similar to ST1B_MOUSESyntaxin 1B (P35B) [R. norvegicus] 1390423_at BE104245 ESTs, Highly8.796017809 9.069358 0.231788 1.208602479 −0.333710591 0.783587436similar to T14792 hypothetical protein DKFZp586G0322. 1 - human(fragment) [H. sapiens] 1398971_at BI283725 ESTs, Moderately 9.3744015639.553263 0.485723 1.13199048 −0.397357886 0.8957128 similar to KIAA0100gene product [Homo sapiens] [H. sapiens] 1388850_at BG671521 ESTs,Moderately 9.638454301 9.957086 0.267318 1.247146979 −0.370218860.693183088 similar to HS9B_RAT Heat shock protein HSP 90-beta (HSP 84)[R. norvegicus] 1390592_at BM389412 ESTs, Moderately 7.9272453898.209323 0.666237 1.215944997 −0.373953853 0.883872321 similar to T14273zinc finger protein 106 - mouse [M. musculus] 1390097_at BI281738 ESTs,Moderately 9.3184521 9.600735 0.359884 1.216117474 −0.2893091370.840945647 similar to Y193_HUMAN Hypothetical protein KIAA0193 [H.sapiens] 1371590_s_at BM386159 ESTs, Weakly 8.508270545 8.290722−0.40327 0.860025673 0.715808502 1.286471079 similar to e- Tropomodulin[Rattus norvegicus] [R. norvegicus] 1390048_at BF408990 ESTs, Weakly7.825368912 8.242474 0.608206 1.335245393 −0.241815196 0.891226221similar to hypothetical protein, MNCb- 4760 [Mus musculus] [M. musculus]1375231_a_at BI281838 ESTs, Weakly 9.410742003 9.628854 0.5309441.163210616 −0.387267422 0.888752574 similar to inhibitor of the Dvl andAxin complex [Rattus norvegicus] [R. norvegicus] 1399079_at AI101659ESTs, Weakly 9.836360668 10.16998 0.396804 1.260170799 −0.2396401850.859334251 similar to SC65 synaptonemal complex protein [Rattusnorvegicus] [R. norvegicus] 1388903_at AI179335 ESTs, Weakly 8.3326383368.114142 −0.5078 0.859460826 0.35815011 1.110966168 similar to t-complex testis expressed 1 [Rattus norvegicus] [R. norvegicus]1373063_at BI277000 ESTs, Weakly 8.697615098 8.502515 −0.430310.87351232 0.463990102 1.15709537 similar to ubiquitin- conjugatingenzyme E2N (homologous to yeast UBC13); bendless protein [Rattusnorvegicus] [R. norvegicus] 1371337_at BG378939 ESTs, Weakly 9.8133325639.642615 −0.3672 0.888400916 0.325054592 1.106521553 similar to S13099cytochrome-c oxidase (EC 1.9.3.1) chain Vlla precursor - rat [R.norvegicus] 1398846_at BE107346 56783 eukaryotic initiation 8.3613764469.008593 0.495006 1.566143804 −0.414497851 0.664667317 factor 5 (elF-5)1387383_at NM_031802 83633 G protein-coupled 9.961560372 9.722226−0.41601 0.847135806 0.740340744 1.292462812 receptor 51 1368401_atM85035 29627 glutamate 9.7450637 10.12056 0.388163 1.297283064−0.370340093 0.761334957 receptor, ionotropic, 2 1388189_at AW52243024416 glutamate 7.922810149 8.369635 0.603662 1.363036876 −0.2823104140.857046994 receptor, metabotropic 3 1387659_at AF245172 83585 guanine8.579875817 8.970425 0.419618 1.310892245 −0.310557432 0.801387052deaminase 1375705_at AI103622 24400 Guanine 11.052428 11.43942 0.6247761.307666247 −0.713058008 0.698548881 nucleotide-binding protein beta 11370053_at BE116953 65040 guanylate kinase 8.181514198 8.416934 0.4021241.177248901 −0.304521974 0.873239295 associated protein 1375532_atAI008792 25587 Inhibitor of DNA 8.470555381 9.278552 0.6556171.750778223 −0.467889277 0.6448088 binding 2, dominant negativehelix-loop-helix protein 1371148_s_at X52017 24503 internexin, alpha8.348395102 8.742675 0.442247 1.314286384 −0.351712988 0.7902458031370865_at BI277627 25179 isocitrate 9.508280943 9.334029 −0.413280.886227042 0.430076542 1.117948633 dehydrogenase 3, gamma 1387071_a_atBE107978 29477 microtubule- 10.20988985 11.06574 0.440253 1.809820398−0.40915131 0.566925482 associated protein tau 1370831_at AY081195 29254monoglyceride 7.997950072 8.519811 0.691492 1.435806237 −0.3709978920.797665306 lipase 1370016_at NM_031070 81734 nel-like 2 9.3664408319.130241 −0.3398 0.84897858 0.629322922 1.313198487 homolog (chicken)1369690_at AI547471 60355 N-ethylmaleimide 9.871860703 9.66198 −0.401310.864608826 0.356371725 1.111739806 sensitive factor 1368993_atNM_020088 56762 neurestin 7.578732705 8.063511 0.624639 1.399370323−0.459690254 0.755545133 1369404_a_at NM_021767 60391 neurexin 17.850829037 8.133737 0.400729 1.216644537 −0.47177386 0.7981221431370058_at NM_031783 83613 neurofilament, light 9.844994746 9.631533−0.42188 0.862465188 0.366920816 1.10425063 polypeptide 1370517_atU18772 266777 neuronal pentraxin 1 9.516316885 9.313932 −0.514920.869112366 0.522032631 1.16884432 1368255_at NM_017354 50864neurotrimin 8.456459057 8.628735 0.372202 1.126834366 −0.3777044190.883893225 1367851_at J04488 25526 Prostaglandin D 11.49214354 11.29404−0.3933 0.871692914 0.290393494 1.108310809 synthase 1398790_atNM_017039 24672 Protein 9.819878116 9.61136 −0.34567 0.8654254230.311060317 1.132692891 phosphatase 2 (formerly 2A), catalytic subunit,alpha isoform 1398825_at D01046 79434 RAB11B, member 8.4678851018.303234 −0.51417 0.892144413 0.494808325 1.119497348 RAS oncogenefamily 1370087_at NM_031718 65158 RAB2, member 8.267117217 8.013845−0.58443 0.838991442 0.408100105 1.123112511 RAS oncogene family1370372_at AF134409 171099 RASD family, 8.98764962 8.822419 −0.404810.891785751 0.417570782 1.12716855 member 2 1369816_at NM_013018 25531Ras-related small 9.593343909 9.380739 −0.35073 0.862977618 0.5468841151.248974009 GTP binding protein 3A 1369958_at NM_022542 64373 rhoB gene8.970515013 8.798449 −0.38451 0.887570983 0.423174482 1.1232725911375421_a_at AI600019 192256 rotein carrying the 9.594165696 10.039020.3913 1.361178681 −0.323072636 0.74473796 RING-H2 sequence motif1375621_at AI575254 261737 sideroflexin 5 7.407218485 7.669141 0.4957381.199075642 −0.417215583 0.848997619 1370224_at BE113920 25125 signaltransducer 7.635173326 7.857439 0.709037 1.166564469 −0.4597544830.890983344 and activator of transcription 3 1388000_at AF021923 84550solute carrier 7.301200621 7.512385 0.309079 1.157637879 −0.251141730.870463115 family 24 (sodium/potassium/ calcium exchanger), member 21368440_at NM_017216 29484 solute carrier 9.398846616 9.93355 0.7496911.448643968 −0.727328652 0.650057604 family 3, member 1 1389986_atAI008409 117556 synaptic vesicle 8.015724584 8.590117 0.6561671.489050598 −0.357264595 0.775227175 glycoprotein 2 b 1369627_at L10362117556 synaptic vesicle 8.663172726 8.82176 0.204444 1.116193334−0.243485248 0.864656842 glycoprotein 2 b 1387662_at L38247 64440synaptotagmin 4 8.677669502 9.157806 0.309263 1.394875371 −0.3348110050.692224654 1369879_a_at NM_019381 24822 Testis enhanced 8.7336027868.580479 −0.38722 0.899301003 0.378082787 1.115748654 gene transcript1368841_at NM_053369 84382 transcription 8.639946736 8.85393 0.4861851.159885847 −0.374241086 0.892103037 factor 4 1386999_at BG380730 56011tyrosine 3- 8.669827204 8.515457 −0.44737 0.898524607 0.5331333441.130282208 monooxgenase/ tryptophan 5 monooxgenase activation protein,beta polypeptide 1398843_at AI411103 58857 vesicle-associated10.04441626 9.889542 −0.34531 0.898210852 0.35733192 1.10078515 membraneprotein, associated protein a 1386909_a_at AF268467 83529voltage-dependent 8.025008371 7.83859 −0.4422 0.87878463 0.4417111221.146114211 anion channel 1

1. A method for determining whether a subject has or is predisposed fora mood disorder, the method comprising the steps of: (i) obtaining abiological sample from a subject; (ii) contacting the sample with areagent that selectively associates with a polynucleotide or polypeptideencoded by a nucleic acid that hybridizes under stringent conditions toa nucleotide sequence of Table 3-6; and (iii) detecting the level ofreagent that selectively associates with the sample, thereby determiningwhether the subject has or is predisposed for a mood disorder.
 2. Themethod of claim 1, wherein the reagent is an antibody.
 3. The method ofclaim 1, wherein the reagent is a nucleic acid.
 4. The method of claim1, wherein the reagent associates with a polynucleotide.
 5. The methodof claim 1, wherein the regent associates with a polypeptide.
 6. Themethod of claim 1, wherein the biological sample is obtained fromamniotic fluid.
 7. The method of claim 1, wherein the mood disorder isselected from the group consisting of bipolar disorder and majordepression disorder.
 8. The method of claim 1, wherein the level ofreagent that associates with the sample is higher than a levelassociated with humans without a mood disorder.
 9. The method of claim1, wherein the level of reagent that associates with the sample is lowerthan a level associated with humans without a mood disorder.
 10. Amethod of identifying a compound for treatment or prevention of a mooddisorder, the method comprising the steps of: (i) contacting thecompound with a polypeptide, the polypeptide encoded by a polynucleotidethat hybridizes under stringent conditions to a nucleic acid sequencecomprising a nucleotide sequence listed in Table 3-6 or a nucleic acidsequence of the PSPHL gene; and (ii) determining the functional effectof the compound upon the polypeptide, thereby identifying a compound fortreatment or prevention of a mood disorder.
 11. The method of claim 10,wherein the contacting step is performed in vitro.
 12. The method ofclaim 10, wherein the polypeptide is expressed in a cell and the cell iscontacted with the compound.
 13. The method of claim 10, the mooddisorder is selected from the group consisting of bipolar disorder andmajor depression disorder.
 14. The method of claim 10, furthercomprising administering the compound to an animal and determining theeffect on the animal.
 15. The method of claim 14, wherein thedetermining step comprises testing the animal's mental function.
 16. Amethod of identifying a compound for treatment of a mood disorder in asubject, the method comprising the steps of: (i) contacting the compoundto a cell, the cell comprising a polynucleotide that hybridizes understringent conditions to a nucleotide sequence listed Tables 3-10 of anucleotide sequence of the PSPHL gene; and (ii) selecting a compoundthat modulates expression of the polynucleotide, thereby identifying acompound for treatment of a mood disorder.
 17. The method of claim 16,wherein the expression of the polynucleotide is enhanced.
 18. The methodof claim 16, wherein the expression of the polynucleotide is decreased.19. The method of claim 16, further comprising administering thecompound to an animal and determining the effect on the animal.
 20. Themethod of claim 19, wherein the determining step comprises testing theanimal's mental function.
 21. The method of claim 16, wherein the mooddisorder is selected from the group consisting of bipolar disorder andmajor depression disorder.
 22. A method of treating a mood disorder in asubject, the method comprising the step of administering to the subjecta therapeutically effective amount of a compound identified using themethod of claim 10 or claim
 16. 23. The method of claim 22, wherein themood disorder is selected from the group consisting of bipolar disorderand major depression disorder.
 24. The method of claim 22, wherein thecompound is a small organic molecule.
 25. A method of treating a mooddisorder in a subject, the method comprising the step of administeringto the subject a therapeutically effective amount of a polypeptide, thepolypeptide encoded by a polynucleotide that hybridizes under stringentconditions to a nucleotide sequence listed in Tables 3-10 or anucleotide sequence of the PSPHL gene.
 26. The method of claim 25,wherein the mood disorder is selected from the group consisting ofbipolar disorder and major depression disorder.
 27. A method of treatinga mood disorder in a subject, the method comprising the step ofadministering to the subject a therapeutically effective amount of anucleic acid, wherein the nucleic acid hybridizes under stringentconditions to a nucleotide sequence listed Table 3-6 or a nucleic acidsequence of the PSPHL gene.
 28. The method of claim 27, wherein the mooddisorder is selected from the group consisting of bipolar disorder andmajor depression disorder.
 29. A method for determining whether asubject has or is predisposed for bipolar disorder, the methodcomprising the steps of: (i) obtaining a biological sample from asubject; (ii) contacting the sample with a reagent that selectivelyassociates with a polynucleotide or polypeptide encoded by the PSPHLgene; and (iii) detecting the level of reagent that selectivelyassociates with the sample, thereby determining whether the subject hasor is predisposed for bipolar disorder.
 30. The method of claim 29,wherein the reagent is an antibody.
 31. The method of claim 29, whereinthe reagent is a nucleic acid.
 32. The method of claim 29, wherein thereagent associates with a PSPHL polynucleotide.
 33. The method of claim29, wherein the reagent associates with a PSPHL mRNA.
 34. The method ofclaim 29, wherein the reagent associates with a PSPHL gene.
 35. Themethod of claim 29, wherein the regent associates with a PSPHLpolypeptide.
 36. The method of claim 29, wherein the biological sampleis obtained from amniotic fluid.
 37. The method of claim 29, wherein thelevel of reagent that associates with the sample is lower than a levelassociated with humans without bipolar disorder.
 38. A method fordetermining whether a subject has or is predisposed for bipolardisorder, the method comprising the steps of: (i) obtaining a biologicalsample from a subject; (ii) contacting the sample with a PCR primer pairthat selectively binds to the PSPHL gene; and (iii) amplifying the PSPHLgene and detecting the amplified gene product in the sample, therebydetermining whether the subject has or is predisposed for bipolardisorder.
 39. A method for determining whether a subject has or ispredisposed for a mood disorder, the method comprising: (i) contactingthe tissue of one or regions of the subject's brain with a detectablylabeled molecule that selectively binds to a gene listed in any ofTables 1-30; (ii) visualizing the distribution of the detectably labeledmolecule in the brain tissue; and (iii) correlating the distribution ofthe detectably labeled molecule with the presence of or predispositionfor a mood disorder in the subject.
 40. The method of claim 39 whereinsaid one or more regions are selected from the group consisting of theanterior cingulate cortex (AnCg), dorsolateral prefrontal cortex(DLPFC), cerebellar cortex (CB), superior temporal gyrus (STG), parietalcortex (PC), and nucleus accumbens (nAcc).
 41. The method of claim 39wherein said labeled molecule is an antisense RNA molecule.
 42. Themethod of claim 39 wherein said contacting occurs in vivo.
 43. Themethod of claim 39 wherein said mood disorder is major depressivedisorder.
 44. The method of claim 39 wherein said mood disorder isbipolar disorder.
 45. A method for determining the course of progressionor regression of a mood disorder: (a) measuring in a biological sample,at a first time, a dysregulated transcript associated with said mooddisorder from Tables 1-30; (b) measuring, at a second time, saiddysregulated transcript in a biological sample from the subject; and (c)comparing the first measurement and the second measurement; wherein thecomparative measurements determine the course of the mood disorder. 46.The method of claim 45 wherein said mood disorder is major depressivedisorder.
 47. The method of claim 45 wherein said mood disorder isbipolar disorder.
 48. A method for treating a subject with a mooddisorder, wherein said mood disorder was diagnosed according to a methodof any of claims 1, 16, 29, or 38, comprising administering atherapeutic formulation which increases the activity of an FGF geneproduct in said subject.
 49. The method of claim 48 wherein saidformulation comprises a recombinant FGF gene product.
 50. The method ofclaim 49 wherein said FGF gene product is FGF-2.
 51. The method of claim48 wherein said formulation comprises a vector capable of expressing anFGF gene product in targeted cells of said subject.
 52. The method ofclaim 51 wherein said FGF gene product is FGF-2.
 53. The method of claim48 wherein said mood disorder is MDD.
 54. A method for determiningwhether a subject has or is predisposed for a mood disorder, the methodcomprising the steps of: (i) obtaining a biological sample from asubject; (ii) contacting the sample with a reagent that selectivelyassociates with a polynucleotide or polypeptide encoded by a nucleicacid that hybridizes under stringent conditions to a nucleotide sequenceof Table 10; and (iii) detecting the level of reagent that selectivelyassociates with the sample, thereby determining whether the subject hasor is predisposed for a mood disorder.
 55. A method for determiningwhether a subject has or is predisposed for a mood disorder, the methodcomprising the steps of: (i) obtaining a biological sample from asubject; (ii) contacting the sample with a reagent that selectivelyassociates with a polynucleotide or polypeptide encoded by a nucleicacid that hybridizes under stringent conditions to a nucleotide sequenceof Tables 18-19; and (iii) detecting the level of reagent thatselectively associates with the sample, thereby determining whether thesubject has or is predisposed for a mood disorder.
 56. A method fordetermining whether a subject has or is predisposed for a mood disorder,the method comprising the steps of: (i) obtaining a biological samplefrom a subject; (ii) contacting the sample with a reagent thatselectively associates with a polynucleotide or polypeptide encoded by anucleic acid that hybridizes under stringent conditions to a nucleotidesequence of Table 20; and (iii) detecting the level of reagent thatselectively associates with the sample, thereby determining whether thesubject has or is predisposed for a mood disorder.
 57. A method fordetermining whether a subject has or is predisposed for a mood disorder,the method comprising the steps of: (i) obtaining a biological samplefrom a subject; (ii) contacting the sample with a reagent thatselectively associates with a polynucleotide or polypeptide encoded by anucleic acid that hybridizes under stringent conditions to a nucleotidesequence of Tables 29-30; and (iii) detecting the level of reagent thatselectively associates with the sample, thereby determining whether thesubject has or is predisposed for a mood disorder.
 58. The method ofclaim 57, wherein said nucleic acid encodes a V-ATPase subunit andwherein said mood disorder is MDD or chronic stress.